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  • Understanding Maq log output

    Hi,

    I have a couple of questions about my Maq map output if anyone knows the answers I'd really appreciate them:

    Code:
    [match_search]  98% processed in 20717.101 sec: 31618863 / 21294334 = 1.485
    [match_search]  99% processed in 20765.187 sec: 28388678 / 20109661 = 1.412
    [match_search] 100% processed in 20768.725 sec: 1164880 / 1048335 = 1.111
    [match_core] sorting the hits and dumping the results...
    [ma_load_reads] loading reads...
    [ma_load_reads] 2000000*2 reads loaded.
    [mapping_count_single] 7, 11, 16, 27
    [maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
    [match_data2mapping] 1922258 out of 4000000 raw reads are mapped with 0 in pairs.
    -- (total, isPE, mapped, paired) = (2000000, 0, 1922258, 0)
    First, what is the "mapping_count_single" - what do these 4 numbers mean?

    Second, this file contained 2,000,000 reads (8 million lines in fastq format), so how come the logfile says x out of 4000000 raw reads are mapped?

    Many Thanks
    Anna

  • #2
    I have a similar issue. My output log reports n_reads*2 because they are paired end, but it looks like that is not the case for your data. My issue is the "x out of n raw reads are mapped" part:

    [match_data2mapping] 1976956 out of 2000000 raw reads are mapped with 1969400 in pairs.
    -- (total, isPE, mapped, paired) = (2000000, 1, 1976956, 1969400)

    What happened to the remaining 23,044 reads? It is not that they are simply unmapped, as I have a number of unmapped reads in my .sam alignment file.

    Any help much appreciated.

    Comment

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