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  • Important For Loops

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    rutwick
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    The document contains bash script commands for: 1) Running a build and indexing process on fasta files labeled AS1a-AS1g. 2) Running a mito_screen_multi process to generate CSV files from the indexes and an input fastq file. 3) Running salmon and kallisto quantification processes on fastq files listed in a CSV, writing outputs. 4) Running additional mito_screen_multi processes on the fastq files. 5) Running grep commands to search SRA files and a text file. 6) Generating a summary CSV by extracting the last line from output files.

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    Important_for_loops

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    The document contains bash script commands for: 1) Running a build and indexing process on fasta files labeled AS1a-AS1g. 2) Running a mito_screen_multi process to generate CSV files from the indexes and an input fastq file. 3) Running salmon and kallisto quantification processes on fastq files listed in a CSV, writing outputs. 4) Running additional mito_screen_multi processes on the fastq files. 5) Running grep commands to search SRA files and a text file. 6) Generating a summary CSV by extracting the last line from output files.

    Copyright:

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

    Important For Loops

    Uploaded by

    rutwick
    The document contains bash script commands for: 1) Running a build and indexing process on fasta files labeled AS1a-AS1g. 2) Running a mito_screen_multi process to generate CSV files from the indexes and an input fastq file. 3) Running salmon and kallisto quantification processes on fastq files listed in a CSV, writing outputs. 4) Running additional mito_screen_multi processes on the fastq files. 5) Running grep commands to search SRA files and a text file. 6) Generating a summary CSV by extracting the last line from output files.

    Copyright:

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

    for char in {a..g} ; do bash build.sh -i ./../AS1${char}.fasta -o .

    /AS1${char}_idx/
    -t 15 ; done

    for char in {a..g} ; do bash mito_screen_multi.sh -l


    ./AS1${char}_idx/mitolib4_w15_uniqglobsort.csv -o AS1${char}_out.csv
    ./../../ID338_DS_11_1ng.fastq ; done

    for char in {a..g} ; do bash mito_screen_multi.sh -l


    ./AS1${char}_idx/mitolib4_w15_uniqglobsort.csv -o AS1${char}_out_counts.csv -r
    int ./../../ID338_DS_11_1ng.fastq ; done

    for fastq in $(cat ./fastq.csv) ; do salmon quant --index rabl+concatdecoy_2_idx/


    --libType A -o ./$(basename $fastq _out) -r $fastq --validateMappings ; done

    for fastq in $(cat ./../fastq.csv) ; do kallisto quant -i rabl+concatdecoy_2.idx -o


    ./$(basename $fastq _out) --single -l 250 -s 1 $fastq ; done

    for fastq in $(cat ./../fastq.csv) ; do kallisto quant -i


    ./../../NRdel/kallisto_NMkeep.idx -o ./$(basename $fastq _out) --single -l 250 -s
    1 $fastq ; done

    for fastq in $(cat ./../fastq.csv) ; do bash mito_screen_multi.sh -l


    ./mitolib3_w31_uniq.csv -o ./out_rpkm/$(basename $fastq _out).csv $fastq ; done

    for fastq in $(cat ./../fastq.csv) ; do bash mito_screen_multi.sh -l


    ./mitolib3_w31_uniq.csv -o ./out_counts/$(basename $fastq _out).csv -r int $fastq ;
    done

    grep -l GSM759889 /misc/enton/cfbi_sra/hs/*/*.txt


    grep -B2 -A3 'HCT20150' Exp_info.txt

    for f in ./* ; do cat $f | tail -1 > temp/$f.csv ; cat temp/* > summary.csv ; done

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