# Some stats
seqkit stats 1*S_*trimmed_ss*.fq.gz
file format type num_seqs sum_len min_len avg_len max_len
16S_ERR1018543_1_trimmed_ssualign.fq.gz FASTQ DNA 26,496 7,348,681 255 277.4 296
16S_ERR1018543_2_trimmed_ssualign.fq.gz FASTQ DNA 26,496 7,851,808 250 296.3 305
16S_ERR1018546_1_trimmed_ssualign.fq.gz FASTQ DNA 31,554 8,748,253 250 277.2 296
16S_ERR1018546_2_trimmed_ssualign.fq.gz FASTQ DNA 31,554 9,373,913 263 297.1 305
18S_ERR1018543_1_trimmed_ssualign.fq.gz FASTQ DNA 10,164 2,818,891 276 277.3 296
18S_ERR1018543_2_trimmed_ssualign.fq.gz FASTQ DNA 10,164 3,013,853 285 296.5 305
18S_ERR1018546_1_trimmed_ssualign.fq.gz FASTQ DNA 4,248 1,177,629 276 277.2 296
18S_ERR1018546_2_trimmed_ssualign.fq.gz FASTQ DNA 4,248 1,262,690 263 297.2 305
seqkit stats 1*S_*trimmed.fq.gz
file format type num_seqs sum_len min_len avg_len max_len
16S_ERR1018543_1_trimmed.fq.gz FASTQ DNA 30,135 8,357,879 255 277.3 296
16S_ERR1018543_2_trimmed.fq.gz FASTQ DNA 30,135 8,931,640 250 296.4 305
16S_ERR1018546_1_trimmed.fq.gz FASTQ DNA 33,381 9,254,697 250 277.2 296
16S_ERR1018546_2_trimmed.fq.gz FASTQ DNA 33,381 9,916,913 263 297.1 305
18S_ERR1018543_1_trimmed.fq.gz FASTQ DNA 6,525 1,809,693 276 277.3 294
18S_ERR1018543_2_trimmed.fq.gz FASTQ DNA 6,525 1,934,021 285 296.4 305
18S_ERR1018546_1_trimmed.fq.gz FASTQ DNA 2,421 671,185 276 277.2 291
18S_ERR1018546_2_trimmed.fq.gz FASTQ DNA 2,421 719,690 285 297.3 305
# Reformat fastq to fasta
reformat.sh in=ERR1018543_1_trimmed.fq.gz in2=ERR1018543_2_trimmed.fq.gz out=ERR1018543_1_trimmed.fasta out2=ERR1018543_2_trimmed.fasta
reformat.sh in=ERR1018546_1_trimmed.fq.gz in2=ERR1018546_2_trimmed.fq.gz out=ERR1018546_1_trimmed.fasta out2=ERR1018546_2_trimmed.fasta
# Prepare ssu-align to be run in parallel
ssu-prep -f -x ERR1018543_1_trimmed.fasta ssu-align_ERR1018543_1 32
ssu-prep -f -x ERR1018543_2_trimmed.fasta ssu-align_ERR1018543_2 32
ssu-prep -f -x ERR1018546_1_trimmed.fasta ssu-align_ERR1018546_1 32
ssu-prep -f -x ERR1018546_2_trimmed.fasta ssu-align_ERR1018546_2 32
# Run ssu-align
./ssu-align_ERR1018543_1.ssu-align.sh
./ssu-align_ERR1018543_2.ssu-align.sh
./ssu-align_ERR1018546_1.ssu-align.sh
./ssu-align_ERR1018546_2.ssu-align.sh
# Get read ids for the 16S and 18S reads identified by ssu-align
PAIR=ERR1018543_1; find ssu-align_"${PAIR}" -regex '.*\(archaea.fa\|bacteria.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_16S_ssu-align.ids
PAIR=ERR1018543_2; find ssu-align_"${PAIR}" -regex '.*\(archaea.fa\|bacteria.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_16S_ssu-align.ids
PAIR=ERR1018546_1; find ssu-align_"${PAIR}" -regex '.*\(archaea.fa\|bacteria.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_16S_ssu-align.ids
PAIR=ERR1018546_2; find ssu-align_"${PAIR}" -regex '.*\(archaea.fa\|bacteria.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_16S_ssu-align.ids
PAIR=ERR1018543_1; find ssu-align_"${PAIR}" -regex '.*\(eukarya.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_18S_ssu-align.ids
PAIR=ERR1018543_2; find ssu-align_"${PAIR}" -regex '.*\(eukarya.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_18S_ssu-align.ids
PAIR=ERR1018546_1; find ssu-align_"${PAIR}" -regex '.*\(eukarya.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_18S_ssu-align.ids
PAIR=ERR1018546_2; find ssu-align_"${PAIR}" -regex '.*\(eukarya.fa\)$' -exec grep '>' {} \; | tr -d '>' | cut -f 1 -d ' ' > "${PAIR}"_18S_ssu-align.ids
# Split reads (we will only use a combination of FWD/REV ids, a more strict approach would be to select only those reads that have been in aligned in FWD/REV)
SSU=16S; SAMPLE=ERR1018543; filterbyname.sh in="${SAMPLE}"_1_trimmed.fq.gz in2="${SAMPLE}"_2_trimmed.fq.gz out="${SSU}"_"${SAMPLE}"_1_trimmed_ssualign.fq.gz out2="${SSU}"_"${SAMPLE}"_2_trimmed_ssualign.fq.gz names=<(cat "${SAMPLE}"_1_18S_ssu-align.ids "${SAMPLE}"_2_18S_ssu-align.ids) include=f
SSU=18S; SAMPLE=ERR1018543; filterbyname.sh in="${SAMPLE}"_1_trimmed.fq.gz in2="${SAMPLE}"_2_trimmed.fq.gz out="${SSU}"_"${SAMPLE}"_1_trimmed_ssualign.fq.gz out2="${SSU}"_"${SAMPLE}"_2_trimmed_ssualign.fq.gz names=<(cat "${SAMPLE}"_1_18S_ssu-align.ids "${SAMPLE}"_2_18S_ssu-align.ids) include=t
SSU=16S; SAMPLE=ERR1018546; filterbyname.sh in="${SAMPLE}"_1_trimmed.fq.gz in2="${SAMPLE}"_2_trimmed.fq.gz out="${SSU}"_"${SAMPLE}"_1_trimmed_ssualign.fq.gz out2="${SSU}"_"${SAMPLE}"_2_trimmed_ssualign.fq.gz names=<(cat "${SAMPLE}"_1_"${SSU}"_ssu-align.ids "${SAMPLE}"_2_"${SSU}"_ssu-align.ids) include=f
SSU=18S; SAMPLE=ERR1018546; filterbyname.sh in="${SAMPLE}"_1_trimmed.fq.gz in2="${SAMPLE}"_2_trimmed.fq.gz out="${SSU}"_"${SAMPLE}"_1_trimmed_ssualign.fq.gz out2="${SSU}"_"${SAMPLE}"_2_trimmed_ssualign.fq.gz names=<(cat "${SAMPLE}"_1_18S_ssu-align.ids "${SAMPLE}"_2_18S_ssu-align.ids) include=t
dada2_input | filtered | denoised | merged | table | no_chimeras | perc_reads_survived | |
---|---|---|---|---|---|---|---|
ERR1018543 | 6525 | 4002 | 3727 | 3629 | 3629 | 3076 | 47.1 |
ERR1018546 | 2421 | 1513 | 1276 | 1229 | 1229 | 1095 | 45.2 |
Total counts: 4,171
Kingdom | n |
---|---|
Eukaryota | 322 |
dada2_input | filtered | denoised | merged | table | no_chimeras | perc_reads_survived | |
---|---|---|---|---|---|---|---|
ERR1018543 | 30135 | 21594 | 20993 | 15563 | 15563 | 12324 | 40.9 |
ERR1018546 | 33381 | 25166 | 24647 | 19719 | 19719 | 15221 | 45.6 |
Total counts: 27,545
Kingdom | n |
---|---|
Archaea | 14 |
Bacteria | 469 |
Eukaryota | 6 |
NA | 6 |
dada2_input | filtered | denoised | merged | table | no_chimeras | perc_reads_survived | |
---|---|---|---|---|---|---|---|
ERR1018543 | 10164 | 5743 | 5457 | 5263 | 5263 | 4701 | 46.3 |
ERR1018546 | 4248 | 2420 | 2162 | 2098 | 2098 | 1901 | 44.8 |
Total counts: 6,602
Kingdom | n |
---|---|
Eukaryota | 388 |
dada2_input | filtered | denoised | merged | table | no_chimeras | perc_reads_survived | |
---|---|---|---|---|---|---|---|
ERR1018543 | 26496 | 20002 | 19443 | 15568 | 15568 | 12328 | 46.5 |
ERR1018546 | 31554 | 24338 | 23812 | 19606 | 19606 | 15075 | 47.8 |
Total counts: 27,403
Kingdom | n |
---|---|
Archaea | 14 |
Bacteria | 465 |
Eukaryota | 6 |
NA | 8 |