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  • sequence coverage format trouble

    Hi everyone!

    I am using bowtie2 to map my reads on scaffolds and I would like to know, is there a way to get a coverage calculation in samtools? I know that I can use BEDTools, but how can I get .bed format from bam? And for my analysis pipeline I need .csv format of coverage information, which is not created in BEDTools.
    Any ideas how I can do this?


    Help!:
    Last edited by OTU; 01-23-2014, 02:13 PM.

  • #2
    There are several solutions on this biostars page including a "samtools depth" one: http://www.biostars.org/p/5165/

    Comment


    • #3
      Thank you!
      However, I wasn't able to find a way to get the information on coverage to be in csv format.
      I used this:
      samtools depth *bamfile* | awk '{sum+=$3} END { print "Average = ",sum/NR}'

      And got the number. Is there a way to get it in csv format?

      Comment


      • #4
        Code:
        samtools depth *bamfile* | awk '{sum+=$3} END { printf("Average,%f\n",sum/NR)}' > some_file.csv
        Will make the output comma separated (csv is just a text file with commas as column separators).

        Comment


        • #5
          That awk script only prints a single number for the whole bam so that is probably not the output OTU is looking for.

          @OTU Are you looking to get a "depth" number for each scaffold?

          Comment

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