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  • Automated script for paired end sequencing

    Hello everybody,

    I have a folder with paired end sequencing data (divided by the asterisk to make group clearly visible here). I would like to run an automated script, which analyses couple by couple (trimming, mapping and so one). I already introduced placeholders for the single steps, but I don't know how to introduce two file (which belong together) at the same time.
    I would be thankful, if someone had a hint for me.

    10pct-0_S3_R1_001.fastq
    10pct-0_S3_R2_001.fastq
    *
    10pct-0_S7_R1_001.fastq
    10pct-0_S7_R2_001.fastq
    *
    10pct-15_S4_R1_001.fastq
    10pct-15_S4_R2_001.fastq
    *
    10pct-15_S8_R1_001.fastq
    10pct-15_S8_R2_001.fastq



    placeholder1='name1'
    placeholder2='name2'
    placeholder3='beginning_of_the_couple_name'

    for placeholder1 in *; do

    trim_galore ../$placeholder1.fastq ../$placeholder2.fastq -q 20 --paired --phred33
    bowtie2 $bowtie_opts $bowtie_index -1 ../$placeholder1.fq -2 ../$placeholder2.fq > $placeholder3.SAM


    samtools view -bS ../$placeholder3.SAM > $placeholder3.BAM

    samtools sort $placeholder3.BAM Sorted_BAMs/sorted_$placeholder3



    done

  • #2
    You don't need to get both names. Just take the first one use regex to change the _R1_ part or get rid of everything from _R1_

    Try this:

    placeholder1='name1'
    placeholder2=`echo $placeholder1 | sed 's/_R1_/_R2_/g'`
    placeholder3=`echo $placeholder1 | sed 's/_R1_\S\+//g'`

    Comment


    • #3
      Thanks a lot for the quick reply!
      Now i run into the trouble, that i only need to choose every 2nd file.
      I wanted to start by listing all files ending with fastq and putting them into a variable, but this files=*.fastq only returns the first file

      Comment


      • #4
        Rather than:

        placeholder1='name1'
        placeholder2='name2'
        placeholder3='beginning_of_the_couple_name'

        for placeholder1 in *; do

        try:


        for placeholder1 in `ls *_R1_*.fastq`; do

        placeholder2=`echo $placeholder1 | sed 's/_R1_/_R2_/g'`
        placeholder3=`echo $placeholder1 | sed 's/_R1_\S\+//g'`
        Last edited by azneto; 01-07-2016, 08:48 AM.

        Comment


        • #5
          So this will start with this file:
          10pct-0_S3_R1_001.fastq
          use it as placeholder and also use this file for the second placeholder:
          ->10pct-0_S3_R2_001.fastq<-
          Nevertheless, as soon as the first round is finished, it will start over with this file again:
          ->10pct-0_S3_R2_001.fastq<-
          I would need something to skip this file.
          Everything i tried so far totally fails...

          Comment


          • #6
            I've noticed that and changed my reply. Check it out:

            for placeholder1 in `ls *_R1_*.fastq`; do

            Comment


            • #7
              Thanks a lot!
              Sorry, i didn't see that you changed your post.
              This solution is not what i thought of, but it's easy and solves the problem
              Thank you.
              Last edited by Alex852013; 01-07-2016, 09:54 AM.

              Comment

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