/usr/share/doc/seqprep/examples/RUNTEST.sh is in seqprep-data 1.3.2-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | #!/bin/bash -x
#To trim these sequences and merge them:
#pushd .. && make clean && make && popd
/usr/bin/seqprep -6 \
-f ./data/multiplex_bad_contam_1.fq.gz \
-r ./data/multiplex_bad_contam_2.fq.gz \
-A GATCGGAAGAGCACACGTCT \
-B AGATCGGAAGAGCGTCGT \
-1 ./out/pe_bad_contam_merged_1.fastq.gz \
-2 ./out/pe_bad_contam_merged_2.fastq.gz \
-s ./out/pe_bad_contam_merged_s.fastq.gz \
-E ./info/alignments_merged.txt.gz
/usr/bin/seqprep -6 \
-f ./data/multiplex_bad_contam_1.fq.gz \
-r ./data/multiplex_bad_contam_2.fq.gz \
-A GATCGGAAGAGCACACGTCT \
-B AGATCGGAAGAGCGTCGT \
-1 ./out/pe_bad_contam_trimmed_1.fastq.gz \
-2 ./out/pe_bad_contam_trimmed_2.fastq.gz \
-E ./info/alignments_trimmed.txt.gz
prog=gzcat
$prog ./out/pe_bad_contam_trimmed_1.fastq.gz | python seqlens.py > ./info/pe_bad_contam_trimmed_1.lenhist.txt
$prog ./out/pe_bad_contam_trimmed_2.fastq.gz | python seqlens.py > ./info/pe_bad_contam_trimmed_2.lenhist.txt
$prog ./out/pe_bad_contam_merged_1.fastq.gz | python seqlens.py > ./info/pe_bad_contam_merged_1.lenhist.txt
$prog ./out/pe_bad_contam_merged_2.fastq.gz | python seqlens.py > ./info/pe_bad_contam_merged_2.lenhist.txt
$prog ./out/pe_bad_contam_merged_s.fastq.gz | python seqlens.py > ./info/pe_bad_contam_merged_s.lenhist.txt
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