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  • Enhancing a classification job

    Hi everyone, hopefully someone can help me with a problem do I have...

    I have Ilumina reads that were mapped against human and mouse, I run picard to separate the Aligned and unaligned reads in two SAMs files (for human and mouse), and also I wrote a perl script to obtain the first column of the SAMs file (the tags) in order to know which reads were shared betwen human and mice (I used the comm command).

    So, the problem is, that I already have a txt file with the tags specific to human and mouse and I want to recover that reads from the SAM files, however it tends to be a problem of order N*M, I test something like:

    grep -f tags.txt reads.sam > output.sam

    However it consumes a huge amount of RAM, and the procces is killed by the sysadmin, in the other hand, I wrote a perl script that opens the SAM file and opens the tags file and compare line per line if is in the tags file but is taking so much time...

    I also was planning to order the tags numerically to enhance the time, but the id is recognized as string and when I sort the tags file it gives something as:
    _9985022_#CTTGTA
    _9986968_#CTTGTA
    _9987522_#CTTGTA
    _999011_#CTTGTA
    _9990461_#CTTGTA
    _9991472_#CTTGTA
    _9994415_#CTTGTA
    _9994569_#CTTGTA
    _999553_#CTTGTA
    _9999187_#CTTGTA

    So, if someone knows a better way to do recover the reads I really would apreciate if tell me how

    Thanks in advance for your help
    Amhed

  • #2
    Solved

    It seems that using a hash consumes much memory, however the process is faster enough.
    Thanks

    Comment

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