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 = {};
$VAR1 = undef;
I saw the source code of the Perl script called in the shell script and couldn't able to solve the problem. Any help and guidance please?
Example: while running "bash parseRepeats.sh"
Begin parsing 137 blast results files
Parsing .... /B_694_Lane1/repeats/blast_0000.gz for blast results
Multiple Paired Reads - Unambiguous. Subject ID: AluSx|SINE1/7SL|Primates READ1: 694_1_1101_4534_2459_R1 READ2: 694_1_1101_4534_2459_R2$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?
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