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What are these BC files for? Should I use them in alignment?

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  • What are these BC files for? Should I use them in alignment?

    Hi, folks. I've started working with some old SOLiD single-ended RNA-seq reads, from 2010 and 2011. I'm using novoalignCS and have the quality files, csfasta files, and an additional fasta-like file with "BC" in the filename. Here's an example of the filenames:

    S1001938CIS_7/primary.20100713155754122/reads/
    solid0015_20100706_S1001938CIS_BC_bcSample1_F3.csfasta
    solid0015_20100706_S1001938CIS_BC_bcSample1_F3.stats
    solid0015_20100706_S1001938CIS_BC_bcSample1_F3_QV.qual
    S1001938CIS_7/primary.20100707172116543/reads/
    solid0015_20100706_S1001938CIS_BC_bcSample1_BC.csfasta

    The F3.csfasta and F3_QV.qual files are as expected, and work fine with novoalignCS.

    The BC.csfasta files have data as follows and I'm completely mystified as to what they are:

    # Wed Jul 7 11:02:39 2010 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid0015/solid0015_20100706_S1001938CIS_BC/bcSample1/results.F1B1/primary.20100707172116543 --name=solid0015_20100706_S1001938CIS_BC_bcSample1 --tag=BC --minlength=5 --mincalls=25 --prefix=G /data/results/solid0015/solid0015_20100706_S1001938CIS_BC/bcSample1/jobs/postPrimerSetPrimary.1505/rawseq
    # Cwd: /home/pipeline
    # Title: solid0015_20100706_S1001938CIS_BC_bcSample1
    # Library:S1001938CIS_7:00313
    >1_223_2_BC 0
    G00313
    >1_238_37_BC 0
    G00313
    >1_240_14_BC 0
    G00313

    Anyone know? Should I be using these BC files in some way? They have extremely little information content.
    Sam Hokin
    Computational Scientist, Carnegie and NCGR

  • #2
    Well, the main thing is your csfasta and qual files work fine.

    Could BC be barcode ? They seemt to be short, as in barcodes, and the format seems to be the csfasta format.

    Not sure I ever saw these in my days of SOLiD adventures, which ended in 2012 (thank god).

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    • #3
      Hey, the data turned out OK and was useful! But yeah, I had to dust off the hard drive the reads were on, it'd been sitting on a shelf for eight years or so.
      Sam Hokin
      Computational Scientist, Carnegie and NCGR

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      • #4
        wow that is some really good work that you've been doing there. I had been closely associated with some projects on Encodeproject on RNA sequence measures.

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