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  • .sam file filtered got normously large,why?

    Hi~~I'm wondering why, after a little filtering (mapping score>=10) of a “.sam” file, just over 20G large, its volumn exploded. The records assumed to be left are less than 10%, which means, the output file is at most 2G large. I checked the results, those ought to be discared were discarded. So why is this happening?
    p.s My output file is either .sam or plain text, doesn't seem to make any difference.

  • #2
    Is it possible that you are using BAM as input?
    If both input and output are text SAM format, could you do 'head -3' on both of them and post here?

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    • #3
      Thx, it was solved! I just wanted to know if SAM is a compressed format.

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