Skip to content
Snippets Groups Projects
Commit 2f1279b7 authored by Simeon Rossmann's avatar Simeon Rossmann
Browse files

Initial_data_dump BigOld

parent 22b26f91
Branches
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 43514 additions and 0 deletions
16S/ASVs_raw.fasta 0 → 100644
+ 13417
− 0
View file @ 2f1279b7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
16S/ASVs_withtax.fasta 0 → 100644
+ 13417
− 0
View file @ 2f1279b7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
16S/R1_error_profile.pdf 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/R2_error_profile.pdf 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/mergers.txt 0 → 100644
+ 10933
− 0
View file @ 2f1279b7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
16S/out.txt 0 → 100644
+ 57
− 0
View file @ 2f1279b7
"reads.in" "reads.out"
"1-16S_S57_L001_R1_001.fastq.gz.trim.fastq.gz" 46270 13206
"10-16S_S76_L001_R1_001.fastq.gz.trim.fastq.gz" 53300 15955
"11-16S_S83_L001_R1_001.fastq.gz.trim.fastq.gz" 56866 16446
"12-16S_S90_L001_R1_001.fastq.gz.trim.fastq.gz" 128 31
"13-16S_S96_L001_R1_001.fastq.gz.trim.fastq.gz" 122259 32560
"14-16S_S102_L001_R1_001.fastq.gz.trim.fastq.gz" 103617 29987
"15-16S_S59_L001_R1_001.fastq.gz.trim.fastq.gz" 41730 11805
"16-16S_S68_L001_R1_001.fastq.gz.trim.fastq.gz" 55508 14621
"17-16S_S77_L001_R1_001.fastq.gz.trim.fastq.gz" 85726 23512
"18-16S_S84_L001_R1_001.fastq.gz.trim.fastq.gz" 51485 13453
"19-16S_S91_L001_R1_001.fastq.gz.trim.fastq.gz" 79403 20036
"2-16S_S66_L001_R1_001.fastq.gz.trim.fastq.gz" 48236 11790
"20-16S_S97_L001_R1_001.fastq.gz.trim.fastq.gz" 49883 13946
"21-16S_S103_L001_R1_001.fastq.gz.trim.fastq.gz" 46529 13184
"22-16S_S60_L001_R1_001.fastq.gz.trim.fastq.gz" 54922 14804
"23-16S_S69_L001_R1_001.fastq.gz.trim.fastq.gz" 70915 21072
"24-16S_S78_L001_R1_001.fastq.gz.trim.fastq.gz" 74330 21814
"25-16S_S85_L001_R1_001.fastq.gz.trim.fastq.gz" 76206 21706
"26-16S_S92_L001_R1_001.fastq.gz.trim.fastq.gz" 33759 7591
"27-16S_S98_L001_R1_001.fastq.gz.trim.fastq.gz" 61522 17206
"28-16S_S104_L001_R1_001.fastq.gz.trim.fastq.gz" 60872 16624
"29-16S_S61_L001_R1_001.fastq.gz.trim.fastq.gz" 45209 13181
"3-16S_S75_L001_R1_001.fastq.gz.trim.fastq.gz" 47439 14783
"30-16S_S70_L001_R1_001.fastq.gz.trim.fastq.gz" 67672 16923
"31-16S_S79_L001_R1_001.fastq.gz.trim.fastq.gz" 78351 20861
"32-16S_S86_L001_R1_001.fastq.gz.trim.fastq.gz" 60483 19273
"33-16S_S93_L001_R1_001.fastq.gz.trim.fastq.gz" 81506 24662
"34-16S_S99_L001_R1_001.fastq.gz.trim.fastq.gz" 23803 7108
"35-16S_S105_L001_R1_001.fastq.gz.trim.fastq.gz" 44053 13134
"36-16S_S111_L001_R1_001.fastq.gz.trim.fastq.gz" 53193 15583
"37-16S_S62_L001_R1_001.fastq.gz.trim.fastq.gz" 53628 15978
"38-16S_S71_L001_R1_001.fastq.gz.trim.fastq.gz" 71885 19550
"39-16S_S80_L001_R1_001.fastq.gz.trim.fastq.gz" 68624 20126
"4-16S_S82_L001_R1_001.fastq.gz.trim.fastq.gz" 45827 12284
"40-16S_S87_L001_R1_001.fastq.gz.trim.fastq.gz" 46286 13802
"41-16S_S94_L001_R1_001.fastq.gz.trim.fastq.gz" 72331 22424
"42-16S_S100_L001_R1_001.fastq.gz.trim.fastq.gz" 60067 17103
"43-16S_S106_L001_R1_001.fastq.gz.trim.fastq.gz" 19250 5646
"44-16S_S112_L001_R1_001.fastq.gz.trim.fastq.gz" 48795 13621
"45-16S_S63_L001_R1_001.fastq.gz.trim.fastq.gz" 55136 17072
"46-16S_S72_L001_R1_001.fastq.gz.trim.fastq.gz" 58429 15010
"5-16S_S89_L001_R1_001.fastq.gz.trim.fastq.gz" 47974 14833
"6-16S_S95_L001_R1_001.fastq.gz.trim.fastq.gz" 35489 12028
"7-16S_S101_L001_R1_001.fastq.gz.trim.fastq.gz" 41208 14696
"8-16S_S58_L001_R1_001.fastq.gz.trim.fastq.gz" 45066 17992
"9-16S_S67_L001_R1_001.fastq.gz.trim.fastq.gz" 19796 5598
"NegK1-16S_S64_L001_R1_001.fastq.gz.trim.fastq.gz" 136 35
"NegK2-16S_S73_L001_R1_001.fastq.gz.trim.fastq.gz" 111 30
"Posk1-16S_S65_L001_R1_001.fastq.gz.trim.fastq.gz" 43382 15413
"Posk2-16S_S74_L001_R1_001.fastq.gz.trim.fastq.gz" 46908 16875
"Posk3-16S_S81_L001_R1_001.fastq.gz.trim.fastq.gz" 38278 15488
"Posk4-16S_S88_L001_R1_001.fastq.gz.trim.fastq.gz" 43850 14785
"V1-16S_S107_L001_R1_001.fastq.gz.trim.fastq.gz" 1806 574
"V2-16S_S108_L001_R1_001.fastq.gz.trim.fastq.gz" 37 12
"V3-16S_S109_L001_R1_001.fastq.gz.trim.fastq.gz" 210 64
"V4-16S_S110_L001_R1_001.fastq.gz.trim.fastq.gz" 90 24
16S/parameters_both25-01-22_1422.txt 0 → 100644
+ 20
− 0
View file @ 2f1279b7
"x"
"Run on 25/01/22 14:22
Path: /home/simeon/Documents/Sunniva_felt21
Samples:
1-16S;10-16S;11-16S;12-16S;13-16S;14-16S;15-16S;16-16S;17-16S;18-16S;19-16S;2-16S;20-16S;21-16S;22-16S;23-16S;24-16S;25-16S;26-16S;27-16S;28-16S;29-16S;3-16S;30-16S;31-16S;32-16S;33-16S;34-16S;35-16S;36-16S;37-16S;38-16S;39-16S;4-16S;40-16S;41-16S;42-16S;43-16S;44-16S;45-16S;46-16S;5-16S;6-16S;7-16S;8-16S;9-16S;NegK1-16S;NegK2-16S;Posk1-16S;Posk2-16S;Posk3-16S;Posk4-16S;V1-16S;V2-16S;V3-16S;V4-16S
Analysis type: both
Database type: /home/simeon/Documents/tax_DBs/16S_databases/bacterial_16S/silva_nr99_v138.1_train_set.fa
dada2 Parameters
maximum expected errors R1: 2
maximum expected errors R2: 2
minimum length: 100
truncate at first instance of Qscore: 2
truncation at length (0 = no trunc) 0,truncation at length (0 = no trunc) 0
minimum overlap during merging: 30
taxonomy bootstrap threshold: 80
Collapse overlapping ASVs: FALSE
Minimum overlap if collapsing overlapping ASVs: 200
Trimming 5' (R1, R2): 10,10"
16S/primers_after_cutadapt_15Samples_25-01-22_1242.txt 0 → 100644
+ 61
− 0
View file @ 2f1279b7
"Sample" "Primer_Read" "Forward" "Complement" "Reverse" "RevComp"
"1-16S_S57_L001_R1_001.fastq.gz.trim.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"1-16S_S57_L001_R1_001.fastq.gz.trim.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"1-16S_S57_L001_R1_001.fastq.gz.trim.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"1-16S_S57_L001_R1_001.fastq.gz.trim.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"10-16S_S76_L001_R1_001.fastq.gz.trim.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"10-16S_S76_L001_R1_001.fastq.gz.trim.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"10-16S_S76_L001_R1_001.fastq.gz.trim.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"10-16S_S76_L001_R1_001.fastq.gz.trim.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"11-16S_S83_L001_R1_001.fastq.gz.trim.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"11-16S_S83_L001_R1_001.fastq.gz.trim.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"11-16S_S83_L001_R1_001.fastq.gz.trim.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"11-16S_S83_L001_R1_001.fastq.gz.trim.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"12-16S_S90_L001_R1_001.fastq.gz.trim.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"12-16S_S90_L001_R1_001.fastq.gz.trim.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"12-16S_S90_L001_R1_001.fastq.gz.trim.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"12-16S_S90_L001_R1_001.fastq.gz.trim.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"13-16S_S96_L001_R1_001.fastq.gz.trim.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"13-16S_S96_L001_R1_001.fastq.gz.trim.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"13-16S_S96_L001_R1_001.fastq.gz.trim.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"13-16S_S96_L001_R1_001.fastq.gz.trim.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"14-16S_S102_L001_R1_001.fastq.gz.trim.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"14-16S_S102_L001_R1_001.fastq.gz.trim.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"14-16S_S102_L001_R1_001.fastq.gz.trim.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"14-16S_S102_L001_R1_001.fastq.gz.trim.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"15-16S_S59_L001_R1_001.fastq.gz.trim.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"15-16S_S59_L001_R1_001.fastq.gz.trim.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"15-16S_S59_L001_R1_001.fastq.gz.trim.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"15-16S_S59_L001_R1_001.fastq.gz.trim.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"16-16S_S68_L001_R1_001.fastq.gz.trim.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"16-16S_S68_L001_R1_001.fastq.gz.trim.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"16-16S_S68_L001_R1_001.fastq.gz.trim.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"16-16S_S68_L001_R1_001.fastq.gz.trim.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"17-16S_S77_L001_R1_001.fastq.gz.trim.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"17-16S_S77_L001_R1_001.fastq.gz.trim.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"17-16S_S77_L001_R1_001.fastq.gz.trim.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"17-16S_S77_L001_R1_001.fastq.gz.trim.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"18-16S_S84_L001_R1_001.fastq.gz.trim.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"18-16S_S84_L001_R1_001.fastq.gz.trim.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"18-16S_S84_L001_R1_001.fastq.gz.trim.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"18-16S_S84_L001_R1_001.fastq.gz.trim.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"19-16S_S91_L001_R1_001.fastq.gz.trim.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"19-16S_S91_L001_R1_001.fastq.gz.trim.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"19-16S_S91_L001_R1_001.fastq.gz.trim.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"19-16S_S91_L001_R1_001.fastq.gz.trim.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"2-16S_S66_L001_R1_001.fastq.gz.trim.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"2-16S_S66_L001_R1_001.fastq.gz.trim.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"2-16S_S66_L001_R1_001.fastq.gz.trim.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"2-16S_S66_L001_R1_001.fastq.gz.trim.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"20-16S_S97_L001_R1_001.fastq.gz.trim.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"20-16S_S97_L001_R1_001.fastq.gz.trim.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"20-16S_S97_L001_R1_001.fastq.gz.trim.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"20-16S_S97_L001_R1_001.fastq.gz.trim.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"21-16S_S103_L001_R1_001.fastq.gz.trim.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"21-16S_S103_L001_R1_001.fastq.gz.trim.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"21-16S_S103_L001_R1_001.fastq.gz.trim.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"21-16S_S103_L001_R1_001.fastq.gz.trim.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"22-16S_S60_L001_R1_001.fastq.gz.trim.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"22-16S_S60_L001_R1_001.fastq.gz.trim.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
"22-16S_S60_L001_R1_001.fastq.gz.trim.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
"22-16S_S60_L001_R1_001.fastq.gz.trim.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
16S/primers_before_cutadapt_15Samples_25-01-22_1235.txt 0 → 100644
+ 61
− 0
View file @ 2f1279b7
"Sample" "Primer_Read" "Forward" "Complement" "Reverse" "RevComp"
"1-16S_S57_L001_R1_001.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"1-16S_S57_L001_R1_001.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 17141
"1-16S_S57_L001_R1_001.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 37796
"1-16S_S57_L001_R1_001.fastq.gz 1-16S_S57_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"10-16S_S76_L001_R1_001.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"10-16S_S76_L001_R1_001.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 21039
"10-16S_S76_L001_R1_001.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 40616
"10-16S_S76_L001_R1_001.fastq.gz 10-16S_S76_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"11-16S_S83_L001_R1_001.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"11-16S_S83_L001_R1_001.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 21223
"11-16S_S83_L001_R1_001.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 45264
"11-16S_S83_L001_R1_001.fastq.gz 11-16S_S83_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"12-16S_S90_L001_R1_001.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"12-16S_S90_L001_R1_001.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 41
"12-16S_S90_L001_R1_001.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 100
"12-16S_S90_L001_R1_001.fastq.gz 12-16S_S90_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"13-16S_S96_L001_R1_001.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"13-16S_S96_L001_R1_001.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 43253
"13-16S_S96_L001_R1_001.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 96146
"13-16S_S96_L001_R1_001.fastq.gz 13-16S_S96_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"14-16S_S102_L001_R1_001.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"14-16S_S102_L001_R1_001.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 38659
"14-16S_S102_L001_R1_001.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 82855
"14-16S_S102_L001_R1_001.fastq.gz 14-16S_S102_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"15-16S_S59_L001_R1_001.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"15-16S_S59_L001_R1_001.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 15570
"15-16S_S59_L001_R1_001.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 33140
"15-16S_S59_L001_R1_001.fastq.gz 15-16S_S59_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"16-16S_S68_L001_R1_001.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"16-16S_S68_L001_R1_001.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 19585
"16-16S_S68_L001_R1_001.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 43453
"16-16S_S68_L001_R1_001.fastq.gz 16-16S_S68_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"17-16S_S77_L001_R1_001.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"17-16S_S77_L001_R1_001.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 31409
"17-16S_S77_L001_R1_001.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 68645
"17-16S_S77_L001_R1_001.fastq.gz 17-16S_S77_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"18-16S_S84_L001_R1_001.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"18-16S_S84_L001_R1_001.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 18012
"18-16S_S84_L001_R1_001.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 40497
"18-16S_S84_L001_R1_001.fastq.gz 18-16S_S84_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"19-16S_S91_L001_R1_001.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"19-16S_S91_L001_R1_001.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 26388
"19-16S_S91_L001_R1_001.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 63824
"19-16S_S91_L001_R1_001.fastq.gz 19-16S_S91_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"2-16S_S66_L001_R1_001.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"2-16S_S66_L001_R1_001.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 15598
"2-16S_S66_L001_R1_001.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 39394
"2-16S_S66_L001_R1_001.fastq.gz 2-16S_S66_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"20-16S_S97_L001_R1_001.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"20-16S_S97_L001_R1_001.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 18346
"20-16S_S97_L001_R1_001.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 39253
"20-16S_S97_L001_R1_001.fastq.gz 20-16S_S97_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"21-16S_S103_L001_R1_001.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"21-16S_S103_L001_R1_001.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 17272
"21-16S_S103_L001_R1_001.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 36766
"21-16S_S103_L001_R1_001.fastq.gz 21-16S_S103_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
"22-16S_S60_L001_R1_001.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
"22-16S_S60_L001_R1_001.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 19986
"22-16S_S60_L001_R1_001.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 43670
"22-16S_S60_L001_R1_001.fastq.gz 22-16S_S60_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
16S/qualityplots_fwd.pdf 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/qualityplots_rev.pdf 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/seqtab.nochim.txt 0 → 100644
+ 57
− 0
View file @ 2f1279b7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
16S/seqtab.nochim_withtax.txt 0 → 100644
+ 2700
− 0
View file @ 2f1279b7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
16S/seqtab.rds 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/seqtab_nochim.rds 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/taxa.rds 0 → 100644
+ 0
− 0
View file @ 2f1279b7
File added
16S/taxonomy_ASVs_NC_R1R2.txt 0 → 100644
+ 2700
− 0
View file @ 2f1279b7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
16S/track.txt 0 → 100644
+ 57
− 0
View file @ 2f1279b7
"input" "filtered" "denoisedF" "denoisedR" "merged" "nonchim" "percent_retained"
"1-16S" 46270 13206 11715 11410 8341 8341 18.0267992219581
"10-16S" 53300 15955 14508 14317 10974 10966 20.5741088180113
"11-16S" 56866 16446 14579 14132 9911 9911 17.428692012802
"12-16S" 128 31 1 1 0 0 0
"13-16S" 122259 32560 29831 29268 21101 21101 17.2592610768941
"14-16S" 103617 29987 27535 27177 20220 20107 19.4051169209686
"15-16S" 41730 11805 9969 9433 6061 6061 14.5243230289959
"16-16S" 55508 14621 12519 12171 8295 8295 14.9437918858543
"17-16S" 85726 23512 20813 20235 13915 13915 16.2319483003989
"18-16S" 51485 13453 11627 11163 7662 7662 14.8820044673206
"19-16S" 79403 20036 18117 17711 13053 13053 16.438925481405
"2-16S" 48236 11790 10105 9819 6745 6745 13.9833319512397
"20-16S" 49883 13946 12045 11751 7791 7791 15.6185474009181
"21-16S" 46529 13184 11568 11281 7867 7867 16.9077349609921
"22-16S" 54922 14804 12997 12584 8983 8983 16.3559229452678
"23-16S" 70915 21072 19469 19173 14774 14667 20.6825072269619
"24-16S" 74330 21814 20172 19838 15650 15549 20.9188752858873
"25-16S" 76206 21706 19968 19692 15090 14997 19.6795527911188
"26-16S" 33759 7591 6503 6386 4385 4385 12.989128824906
"27-16S" 61522 17206 15327 15016 10955 10920 17.7497480576054
"28-16S" 60872 16624 14919 14521 10993 10993 18.0592062031804
"29-16S" 45209 13181 11662 11288 8339 8339 18.4454422791922
"3-16S" 47439 14783 13093 12865 9269 9256 19.5113724994203
"30-16S" 67672 16923 15262 15021 11717 11672 17.2479016432202
"31-16S" 78351 20861 19391 19086 14910 14794 18.8816990210718
"32-16S" 60483 19273 17241 16909 12688 12688 20.9777954135873
"33-16S" 81506 24662 22828 22393 17401 17305 21.2315657742988
"34-16S" 23803 7108 5887 5741 4159 4159 17.472587488972
"35-16S" 44053 13134 11971 11790 9095 9068 20.5842961886818
"36-16S" 53193 15583 14338 14059 11140 11140 20.9426052300115
"37-16S" 53628 15978 14820 14341 11449 11263 21.0020884612516
"38-16S" 71885 19550 17813 17743 13506 13506 18.7883424914794
"39-16S" 68624 20126 18623 18246 13872 13872 20.2145022149685
"4-16S" 45827 12284 11150 10790 8328 8308 18.1290505597137
"40-16S" 46286 13802 12505 12132 9339 9339 20.1767273041524
"41-16S" 72331 22424 20650 20317 15775 15775 21.8094592913135
"42-16S" 60067 17103 15512 15242 12102 12102 20.147501956149
"43-16S" 19250 5646 4815 4667 3552 3552 18.4519480519481
"44-16S" 48795 13621 12105 11812 8816 8816 18.06742494108
"45-16S" 55136 17072 15616 15048 11988 11988 21.7426001160766
"46-16S" 58429 15010 13552 13203 10176 10176 17.4160091735268
"5-16S" 47974 14833 14005 13832 11002 10627 22.1515821069746
"6-16S" 35489 12028 11152 11026 8412 8298 23.3818929809237
"7-16S" 41208 14696 14196 14057 10811 10360 25.1407493690546
"8-16S" 45066 17992 17532 17510 13249 12524 27.790351928283
"9-16S" 19796 5598 4734 4562 3426 3426 17.3065265710244
"NegK1-16S" 136 35 28 19 19 19 13.9705882352941
"NegK2-16S" 111 30 25 18 18 18 16.2162162162162
"Posk1-16S" 43382 15413 15394 15293 11909 11810 27.2232723249274
"Posk2-16S" 46908 16875 16852 16759 13097 12925 27.5539353628379
"Posk3-16S" 38278 15488 15469 15423 11926 11829 30.9028684884268
"Posk4-16S" 43850 14785 14752 14649 11565 11496 26.2166476624857
"V1-16S" 1806 574 535 496 407 407 22.5359911406423
"V2-16S" 37 12 5 5 5 5 13.5135135135135
"V3-16S" 210 64 46 37 21 21 10
"V4-16S" 90 24 13 15 13 13 14.4444444444444
ITS1/ASVs_raw.fasta 0 → 100644
+ 17
− 0
View file @ 2f1279b7
>ASV1
CCACTTCCAATATCTGTGATGGTAATTGTGTGCCAGCCGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACT
GGGCGTAAAGCGTGCGCAGGCGGTTGTGCAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAATTGCATTTGTGACTG
CACGGCTAGAGTGTGTCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGATATGTGGAGGAATACCGATGG
CGAAGGCAGCCCCCTGGGATAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTCGTAGTC
CGGCTGGCTGACTATCTCGGATGCCGTCT
>ASV2
CGGTAATTCCAGCTCCACTAGCGTAAAATATTACTGCTGCGGTTAAAAAGCTCGTAGTTGAATTTAGTCGGGTCGTGTTC
CTGTCGGTATGACGGCGAGAAATCGCTAACTGGCGTTGGTTCACACCGATTAGCTAGCCTGCTGTTGGTCTTCGGATCTT
CGGTGGCTAGCGAGTTACTTTGATCAAATCAGAGTGCTCAAAACGGGCGAAAGCTTGTATGATATCTCGAGGAATAACAG
AAGAGGACTTCGGTTCTATTTGTTGGTTCCTGAATCGTTTAATGGTTAAGAGGGACAATTCGGGGGCAAACGTATCCTTG
CGCGAGGGGTGAAATCCGTAGACCGTGAGGAGACGACCAATAGCGAAAGCATTTGCCAAGAATGTCTCCATTAATCAAGA
ACGAAAGTCAGAGGTTCGAAGGCGA
>ASV3
GTAGGTGAACCTGCGGAAGGATCATTAACGAGTTTTATACATTAGTATAATCTTCATCCATAACACCTGTGAACTTTACA
TTAACTTTTGCTTTGGCTGGACGTAAAAAACCTAGCCAAAGGATTAAAATCAAAACCTTTTATTTAAAAACCTAATGTCT
GAAACTAAAAATATTTAATTATTTAAAACTTTCAACAACG
ITS1/ASVs_withtax.fasta 0 → 100644
+ 17
− 0
View file @ 2f1279b7
>ASV1||k__Fungi;NA;NA;NA;NA;NA;NA
CCACTTCCAATATCTGTGATGGTAATTGTGTGCCAGCCGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACT
GGGCGTAAAGCGTGCGCAGGCGGTTGTGCAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAATTGCATTTGTGACTG
CACGGCTAGAGTGTGTCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGATATGTGGAGGAATACCGATGG
CGAAGGCAGCCCCCTGGGATAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTCGTAGTC
CGGCTGGCTGACTATCTCGGATGCCGTCT
>ASV2||k__Fungi;NA;NA;NA;NA;NA;NA
CGGTAATTCCAGCTCCACTAGCGTAAAATATTACTGCTGCGGTTAAAAAGCTCGTAGTTGAATTTAGTCGGGTCGTGTTC
CTGTCGGTATGACGGCGAGAAATCGCTAACTGGCGTTGGTTCACACCGATTAGCTAGCCTGCTGTTGGTCTTCGGATCTT
CGGTGGCTAGCGAGTTACTTTGATCAAATCAGAGTGCTCAAAACGGGCGAAAGCTTGTATGATATCTCGAGGAATAACAG
AAGAGGACTTCGGTTCTATTTGTTGGTTCCTGAATCGTTTAATGGTTAAGAGGGACAATTCGGGGGCAAACGTATCCTTG
CGCGAGGGGTGAAATCCGTAGACCGTGAGGAGACGACCAATAGCGAAAGCATTTGCCAAGAATGTCTCCATTAATCAAGA
ACGAAAGTCAGAGGTTCGAAGGCGA
>ASV3||k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Saccharomycetales_fam_Incertae_sedis;g__Nadsonia;s__commutata
GTAGGTGAACCTGCGGAAGGATCATTAACGAGTTTTATACATTAGTATAATCTTCATCCATAACACCTGTGAACTTTACA
TTAACTTTTGCTTTGGCTGGACGTAAAAAACCTAGCCAAAGGATTAAAATCAAAACCTTTTATTTAAAAACCTAATGTCT
GAAACTAAAAATATTTAATTATTTAAAACTTTCAACAACG
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment