Changes between Version 5 and Version 6 of SOPs/gzipping


Ignore:
Timestamp:
12/02/13 13:59:54 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/gzipping

    v5 v6  
    2020
    2121# Trim low-quality bases at end of reads \\
    22 gunzip -c fastq/My_sample.noVec.qgt20.1.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -z -o fastq/My_sample.noVec.qgt20.t.1.fq.gz \\
    23 gunzip -c fastq/My_sample.noVec.qgt20.2.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -z -o fastq/My_sample.noVec.qgt20.t.2.fq.gz \\
     22gunzip -c fastq/My_sample.noVec.qgt20.1.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -o fastq/My_sample.noVec.qgt20.t.1.fq \\
     23gunzip -c fastq/My_sample.noVec.qgt20.2.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -o fastq/My_sample.noVec.qgt20.t.2.fq \\
    2424
    2525# After trimming, get reads that are still paired (and output as regular fastq for next (bowtie) step) \\
    26 /nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastqgz.pl fastq/My_sample.noVec.qgt20.t.1.fq.gz fastq/My_sample.noVec.qgt20.t.2.fq.gz
     26# We hope to modify cmpfastq.pl to accept gz files as input \\
     27/nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastq.pl fastq/My_sample.noVec.qgt20.t.1.fq fastq/My_sample.noVec.qgt20.t.2.fq
    2728
    2829# Map paired reads with bowtie \\