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  • Coding Corset

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    Awawawawa Uwuwuwuwu
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    The document contains commands to build indexes for three datasets (trinityFalShtKrt.cdhit, trinityFalSht.cdhit, and trinityFalKrt.cdhit) using bowtie2. It then runs bowtie2 to map reads from the three datasets to the indexes and converts the alignments to BAM files. Corset is run to cluster the reads in each BAM file, and the reads for selected clusters are extracted.

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    coding corset

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    The document contains commands to build indexes for three datasets (trinityFalShtKrt.cdhit, trinityFalSht.cdhit, and trinityFalKrt.cdhit) using bowtie2. It then runs bowtie2 to map reads from the three datasets to the indexes and converts the alignments to BAM files. Corset is run to cluster the reads in each BAM file, and the reads for selected clusters are extracted.

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    © All Rights Reserved
    Download as TXT, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    5 views1 page

    Coding Corset

    Uploaded by

    Awawawawa Uwuwuwuwu
    The document contains commands to build indexes for three datasets (trinityFalShtKrt.cdhit, trinityFalSht.cdhit, and trinityFalKrt.cdhit) using bowtie2. It then runs bowtie2 to map reads from the three datasets to the indexes and converts the alignments to BAM files. Corset is run to cluster the reads in each BAM file, and the reads for selected clusters are extracted.

    Copyright:

    © All Rights Reserved
    Download as TXT, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    of 1

    bowtie2-build --threads 20 trinityFalShtKrt.cdhit trinityFalShtKrt.cdhit.

    index &&
    bowtie2-build --threads 20 trinityFalSht.cdhit trinityFalSht.cdhit.index &&
    bowtie2-build --threads 20 trinityFalKrt.cdhit trinityFalKrt.cdhit.index && ls -l
    && bowtie2 -p 22 -x trinityFalShtKrt.cdhit.index -1 Sht-01_fal_1.fq,Krt-
    01_fal_1.fq -2 Sht-01_fal_2.fq,Krt-01_fal_2.fq -S trinityFalShtKrt.cdhit.sam &&
    bowtie2 -p 22 -x trinityFalSht.cdhit.index -1 Sht-01_fal_1.fq -2 Sht-01_fal_2.fq
    -S trinityFalSht.cdhit.sam && bowtie2 -p 22 -x trinityFalKrt.cdhit.index -1 Krt-
    01_fal_1.fq -2 Krt-01_fal_2.fq -S trinityFalKrt.cdhit.sam &&
    /usr/local/NGS/samtools-1.9/samtools view -S -b trinityFalShtKrt.cdhit.sam >
    trinityFalShtKrt.cdhit.bam && /usr/local/NGS/samtools-1.9/samtools view -S -b
    trinityFalSht.cdhit.sam > trinityFalSht.cdhit.bam &&
    /usr/local/NGS/samtools-1.9/samtools view -S -b trinityFalKrt.cdhit.sam >
    trinityFalKrt.cdhit.bam && ls -l && /usr/local/NGS/corset-1.07-linux64/corset -r
    true-stop trinityFalShtKrt.cdhit.bam && /usr/local/NGS/corset-1.07-linux64/corset -
    r true-stop trinityFalSht.cdhit.bam && /usr/local/NGS/corset-1.07-linux64/corset -r
    true-stop trinityFalKrt.cdhit.bam &&

    /usr/local/NGS/corset-1.07-linux64/corset -m 0 -i corset
    trinityFalShtKrt.cdhit.bam.corset-reads
    /usr/local/NGS/corset-1.07-linux64/corset -m 0 -i corset
    trinityFalSht.cdhit.bam.bam.corset-reads
    /usr/local/NGS/corset-1.07-linux64/corset -m 0 -i corset
    trinityFalKrt.cdhit.bam.corset-reads

    ../../fetchClusterSeqs.py -i ../trinityNl.CAP3.cdhit -t counts_x.txt -o


    contigs_of_interest.fasta -c clusters.txt

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