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  • sindrle
    Senior Member
    • Aug 2013
    • 266
    #1

    Analyze coverage on each chromosome

    Hi!
    We have sequenced up some single cells, but now I have to check the amount of rRNA/tRNA/chrM and how much coverage we actually have on known genes (per chromosome or something similar).

    How do you people usually do this? I have been playing around with Igvtools count etc. But I want hard data i.e. 60% chrM reads and X reads on chr1 etc.

    We only have 20 mill. reads per sample and only 8 samples. What is considered ok coverage with regards to genes we want to analyze (non-rRNA/tRNA/chrM)?


    Thanks!
    Tags: None
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    Bedtools coverageBed should suffice. Search for threads on the forum that cover this with examples etc.

    Comment

    • sindrle
      Senior Member
      • Aug 2013
      • 266
      #3
      Oh, I just didnt use the correct search terms, thanks!

      I have also played around a bit with Seqmonk, but I didnt quite like it at first glance.. Maybe BEDtools is the way to go.

      This one is good:

      Counting read depth using bedtools - SEQanswers
      http://seqanswers.com/forums/showthread.php?t=41110&highlight=coverageBed
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

      Comment

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