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  • coverageBed using paired-end fastq as input

    I am new to Illumina data with more experience with Ion Torrent data. Recently, I have some fastq files and before:

    CoverageBed using a bam:
    Code:
     coverageBed -d -a targets.bed -b IonXpress_.bam > IonXpress_output.txt

    Now that I have 2 paired-end fastq files:
    S5_R1.fastq
    S5_R2.fastq

    How do I use them with coverageBed? Thank you .

  • #2
    And you are back

    You seem to have overlooked the step of having to trim/align the fastq files to get an alignment file (BAM) before you can think about coverageBed.

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    • #3
      I am totally new to Illumina data and admit I did not think of that step. Do you have any recommendations far as what to use or where to begin? Thank you .

      Comment


      • #4
        Originally posted by cmccabe View Post
        I am totally new to Illumina data and admit I did not think of that step. Do you have any recommendations far as what to use or where to begin? Thank you .
        What kind of data is this? I will suggest starting with BBDuk (to trim data/look for adapters) and then BBMap (to align) but other aligners will work as well.

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        • #5
          This is Illumina paired-end data from a NextSeq. I will give those to applications a try. Thank you .

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          • #6
            Originally posted by cmccabe View Post
            This is Illumina paired-end data from a NextSeq. I will give those to applications a try. Thank you .
            Is it DNAseq, RNASeq, ChIP_seq .. "what-seq" kind of data. BBMap would work for all of those but downstream analysis will be different.

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            • #7
              It is DNA-seq data. Thank you .

              I spent some time reading and learning some programing. Thank you for your helpful posts
              Last edited by cmccabe; 10-28-2015, 02:34 PM.

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