Use of uninitialized value $refBase in pattern match (m//)

[Wilfried Guiblet]

Hello CTK user group,

I am having an issue running parseAlignment.pl on data mapped by STAR to a transcriptome reference:

parseAlignment.pl -v --map-qual 1 --min-len 18 --mutation-file $f.Transcriptome.mutation.txt $f.Transcriptome.sam.gz $f.Transcriptome.tag.bed

0 ...

Use of uninitialized value $refBase in pattern match (m//) at parseAlignment.pl line 370, <$fin> line 3095.

negative score:$VAR1 = {

          'QNAME' => 'VH00270:4:AAANLCLM5:1:1502:18288:523981:N:0:1rbc:GTCACGGAG',

          'MRNM' => '*',

          'TAGS' => 'NH:i:1 HI:i:1',

          'MPOS' => '0',

          'MAPQ' => 255,

          'FLAG' => '0',

          'SEQ' => 'AGTGGAGGTCAGAAGAGAGTTGCATTCTCTGGGACTAGAG',

          'QUAL' => 'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;C',

          'POS' => 1950,

          'CIGAR' => '19M2D21M',

          'RNAME' => 'ENSMUST00000194301.5',

          'ISIZE' => '0'

        };

 

 at parseAlignment.pl line 457, <$fin> line 3095.

   main::samToBedAndMutation(HASH(0x8f7968)) called at parseAlignment.pl line 104

 

I think this is due to the D in the CIGAR string, but this issue did not happen when using reads mapped to the genome.

Would anyone know what I am doing wrong?

Thanks in advance!

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