ALEXA-seq blast output parsing error

[demis001]

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?

[Emilie]

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