Changes between Version 65 and Version 66 of SOPs/qc_shortReads


Ignore:
Timestamp:
10/04/24 14:10:43 (3 months ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
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  • SOPs/qc_shortReads

    v65 v66  
    9898
    9999{{{
    100    sbatch -p 20 --wrap "/nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastq.pl s_8_1_sequence.txt s_8_2_sequence.txt"  # fastq inputs
     100   sbatch --partition=20 --job-name=cmpfastq --mem=16G --wrap "/nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastq.pl s_8_1_sequence.txt s_8_2_sequence.txt"  # fastq inputs
    101101}}}
    102102
    … …  
    189189
    190190{{{
    191 sbatch -p 20 --wrap "fastq_quality_trimmer -v -t 20 -l 25 -i input.fastq -o output.fastq"  # fastq input and output
    192 sbatch -p 20 --wrap "gunzip -c input.fastq.gz | fastq_quality_trimmer -v -t 20 -l 25 -z -o output.fastq.gz"  # fastq.gz input and output
     191sbatch --partition=20 --job-name=trim --mem=16G --wrap "fastq_quality_trimmer -v -t 20 -l 25 -i input.fastq -o output.fastq"  # fastq input and output
     192sbatch --partition=20 --job-name=trim --mem=16G --wrap "gunzip -c input.fastq.gz | fastq_quality_trimmer -v -t 20 -l 25 -z -o output.fastq.gz"  # fastq.gz input and output
    193193
    194194   [-t N]       = Quality threshold - nucleotides with lower
    … …  
    231231    {{{
    232232    # single-end reads
    233     sbatch -p 20 --wrap "cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT -o Reads_noAdapter.fastq Reads.fastq"
     233    sbatch --partition=20 --job-name=cutadapt --mem=16G --wrap "cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT -o Reads_noAdapter.fastq Reads.fastq"
    234234
    235235    In the above command:
    … …  
    238238
    239239    # paired-end reads
    240     sbatch -p 20 --wrap "cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT -o Reads_trimmed.1.fq -p Reads_trimmed.2.fq Reads.1.fq Reads.2.fq"
     240    ssbatch --partition=20 --job-name=cutdapt --mem=16G --wrap "cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT -o Reads_trimmed.1.fq -p Reads_trimmed.2.fq Reads.1.fq Reads.2.fq"
    241241
    242242    # use --quality-base=64 option for Phred+64 (Illumina 1.5)
    … …  
    270270    * Sample command:
    271271{{{
    272 sbatch -p 20 --wrap "fastx_clipper -a CTGTAGGCACCATCAAT -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt"  # fastq input and output
    273 sbatch -p 20 --wrap "gunzip -c s2_sequence.txt | fastx_clipper -a CTGTAGGCACCATCAAT -v -l 22 -z -o s2_sequence_noLinker.txt.gz"  # fastq.gz input and output
     272sbatch --partition=20 --job-name=clip --mem=16G --wrap "fastx_clipper -a CTGTAGGCACCATCAAT -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt"  # fastq input and output
     273sbatch --partition=20 --job-name=clip --mem=16G --wrap "gunzip -c s2_sequence.txt | fastx_clipper -a CTGTAGGCACCATCAAT -v -l 22 -z -o s2_sequence_noLinker.txt.gz"  # fastq.gz input and output
    274274
    275275