Changes between Version 2 and Version 3 of SOPs/gzipping


Ignore:
Timestamp:
11/15/13 12:22:47 (11 years ago)
Author:
gbell
Comment:

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  • SOPs/gzipping

    v2 v3  
    22
    33# Untar from solexa_public, gunzip, and gzip \\
    4 tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.1.tar.gz | gzip -f > fastq/My_sample_2.1.fq.gz \\
    5 tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.2.tar.gz | gzip -f > fastq/My_sample_2.2.fq.gz \\
     4tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.1.tar.gz | gzip -f > fastq/My_sample.1.fq.gz \\
     5tar -xOzf /lab/solexa_public/LAB/RUN/QualityScore/Foo.2.tar.gz | gzip -f > fastq/My_sample.2.fq.gz \\
    66
    77# Run FastQC \\
    8 fastqc fastq/My_sample_2.1.fq.gz \\
    9 fastqc fastq/My_sample_2.2.fq.gz \\
     8fastqc fastq/My_sample.1.fq.gz \\
     9fastqc fastq/My_sample.2.fq.gz \\
    1010
    1111# Trim adapters \\
    12 gunzip -c fastq/My_sample_2.1.fq.gz | fastx_clipper -v -z -l 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -o fastq/My_sample_2.noVec.1.fq.gz \\
    13 gunzip -c fastq/My_sample_2.2.fq.gz | fastx_clipper -v -z -l 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -o fastq/My_sample_2.noVec.2.fq.gz \\
    14 fastqc fastq/My_sample_2.noVec.1.fq.gz \\
    15 fastqc fastq/My_sample_2.noVec.2.fq.gz \\
     12gunzip -c fastq/My_sample.1.fq.gz | fastx_clipper -v -z -l 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -o fastq/My_sample.noVec.1.fq.gz \\
     13gunzip -c fastq/My_sample.2.fq.gz | fastx_clipper -v -z -l 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -o fastq/My_sample.noVec.2.fq.gz \\
     14fastqc fastq/My_sample.noVec.1.fq.gz \\
     15fastqc fastq/My_sample.noVec.2.fq.gz \\
    1616
    1717# Drop reads of low quality \\
    18 gunzip -c fastq/My_sample_2.noVec.1.fq.gz | fastq_quality_filter -v -q 20 -p 75 -z -o fastq/My_sample_2.noVec.qgt20.1.fq.gz \\
    19 gunzip -c fastq/My_sample_2.noVec.2.fq.gz | fastq_quality_filter -v -q 20 -p 75 -z -o fastq/My_sample_2.noVec.qgt20.2.fq.gz \\
     18gunzip -c fastq/My_sample.noVec.1.fq.gz | fastq_quality_filter -v -q 20 -p 75 -z -o fastq/My_sample.noVec.qgt20.1.fq.gz \\
     19gunzip -c fastq/My_sample.noVec.2.fq.gz | fastq_quality_filter -v -q 20 -p 75 -z -o fastq/My_sample.noVec.qgt20.2.fq.gz \\
    2020
    2121# Trim low-quality bases at end of reads \\
    22 gunzip -c fastq/My_sample_2.noVec.qgt20.1.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -z -o fastq/My_sample_2.noVec.qgt20.t.1.fq.gz \\
    23 gunzip -c fastq/My_sample_2.noVec.qgt20.2.fq.gz | fastq_quality_trimmer -v -t 20 -l 30 -z -o fastq/My_sample_2.noVec.qgt20.t.2.fq.gz \\
     22gunzip -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 \\
     23gunzip -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 \\
    2424
    2525# After trimming, get reads that are still paired (and output as regular fastq) \\
    26 /nfs/BaRC_Public/BaRC_code/Perl/cmpfastq/cmpfastqgz.pl fastq/My_sample_2.noVec.qgt20.t.1.fq.gz fastq/My_sample_2.noVec.qgt20.t.2.fq.gz
     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
    2727
    2828# Map paired reads with bowtie \\
    29 # THIS STEP CANNOT USE GZ FILES \\
    30 bowtie -l 30 -n 1 -X 1000 --best -S /nfs/genomes/a.thaliana_TAIR_10/bowtie/tair10_SI -1 fastq/My_sample_2.noVec.qgt20.t.1.fq-common.out -2 fastq/My_sample_2.noVec.qgt20.t.2.fq-common.out mapped_reads/My_sample_2.30.1.sam
     29# '''bowtie cannot use gzipped input files''' \\
     30bowtie -l 30 -n 1 -X 1000 --best -S /nfs/genomes/GENOME/bowtie/INDEX -1 fastq/My_sample.noVec.qgt20.t.1.fq-common.out -2 fastq/My_sample.noVec.qgt20.t.2.fq-common.out mapped_reads/My_sample.30.1.sam
    3131
    3232# Sort and index mapped reads \\
    33 /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl mapped_reads/My_sample_2.30.1.sam \\
     33/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl mapped_reads/My_sample.30.1.sam \\
    3434# Delete SAM file (since BAM file has all the same info) \\
    35 rm -f mapped_reads/My_sample_2.30.1.sam \\
     35rm -f mapped_reads/My_sample.30.1.sam \\
    3636
    3737# Get summary counts \\
    38 zcat fastq/My_sample_2.1.fq.gz | echo $((`wc -l`/4)) \\
    39 zcat fastq/My_sample_2.noVec.1.fq.gz | echo $((`wc -l`/4)) \\
    40 zcat fastq/My_sample_2.noVec.2.fq.gz | echo $((`wc -l`/4)) \\
    41 zcat fastq/My_sample_2.noVec.qgt20.1.fq.gz | echo $((`wc -l`/4)) \\
    42 zcat fastq/My_sample_2.noVec.qgt20.2.fq.gz | echo $((`wc -l`/4)) \\
    43 more fastq/My_sample_2.noVec.qgt20.t.1.fq | echo $((`wc -l`/4)) \\
    44 more fastq/My_sample_2.noVec.qgt20.t.2.fq | echo $((`wc -l`/4)) \\
    45 zmore fastq/My_sample_2.noVec.qgt20.t.1.fq-common.out.gz | echo $((`wc -l`/4)) \\
    46 samtools flagstat mapped_reads/My_sample_2.30.1.sorted.bam > mapped_reads/My_sample_2.30.1.flagstat.txt \\
    47 grep ' mapped (' mapped_reads/My_sample_2.30.1.flagstat.txt
     38zcat fastq/My_sample.1.fq.gz | echo $((`wc -l`/4)) \\
     39zcat fastq/My_sample.noVec.1.fq.gz | echo $((`wc -l`/4)) \\
     40zcat fastq/My_sample.noVec.2.fq.gz | echo $((`wc -l`/4)) \\
     41zcat fastq/My_sample.noVec.qgt20.1.fq.gz | echo $((`wc -l`/4)) \\
     42zcat fastq/My_sample.noVec.qgt20.2.fq.gz | echo $((`wc -l`/4)) \\
     43more fastq/My_sample.noVec.qgt20.t.1.fq | echo $((`wc -l`/4)) \\
     44more fastq/My_sample.noVec.qgt20.t.2.fq | echo $((`wc -l`/4)) \\
     45zmore fastq/My_sample.noVec.qgt20.t.1.fq-common.out.gz | echo $((`wc -l`/4)) \\
     46samtools flagstat mapped_reads/My_sample.30.1.sorted.bam > mapped_reads/My_sample.30.1.flagstat.txt \\
     47grep ' mapped (' mapped_reads/My_sample.30.1.flagstat.txt
    4848
    4949