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  • ALEXA-seq blast output parsing error

    I am using ALEXA-seq for paired end RNA-seq differential splicing analysis and got an error while parsing BLAST output of the first *.gz file. It seems the error occurred while parsing Repeats, Introns and Intergenic. I used the recommended versions of Blastall and BWA and didn't expect output format difference. The error looks like this...

    Example: while running "bash parseRepeats.sh"
    Begin parsing 137 blast results files

    Parsing .... /B_694_Lane1/repeats/blast_0000.gz for blast results
    Multiple Paired Reads - Unambiguous. Subject ID: AluSx|SINE1/7SL|Primates READ1: 694_1_1101_4534_2459_R1 READ2: 694_1_1101_4534_2459_R2$VAR1 = {};
    $VAR1 = undef;

    I saw the source code of the Perl script called in the shell script and couldn't able to solve the problem. Any help and guidance please?

  • #2
    Hi,
    This problem might be due to the read ID.
    At two different locations in the parseBlastResults_*.pl files, the read IDs are extracted using this regular expression:
    $read_id =~ /([a-zA-Z0-9]+_\d+_\d+_\d+_\d+)_(R\d)/

    Did you look at the read ID in the file blast_0000.gz? Does the read ID match the pattern?
    You could try to modify these lines in the perl scripts to match your read names, or change the read names.

    Emilie

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