Hi all,
I have some problems with my pileup file. I used Tophat to map my RNA-seq reads and samtools mpileup to generate my output file. An example of the first 5 columns (without the column for base qualities) is as follows:
chr1 155743 N 15 <<<>>><>>>>><Gg
chr1 155744 N 15 <<<>>><>>>>><Tt
chr1 155745 N 15 <<<>>><>>>>><Aa
chr1 155746 N 15 <<<>>><>>>>><Cc
chr1 155747 N 15 <<cCCCcCCCCCcCc
chr1 155748 N 15 <<tTTTtTTTTTtTt
chr1 155749 N 15 <<gGGGgGGGGGgGg
chr1 155750 N 15 <<aAAAaAAAAAaAa
It's showing N because I did not use a reference index. However, my question is why there are < and > in the column for read bases? I'm thinking they might refer to reads that span exon-exon junctions. Has anyone else encountered them before?
Thanks.
I have some problems with my pileup file. I used Tophat to map my RNA-seq reads and samtools mpileup to generate my output file. An example of the first 5 columns (without the column for base qualities) is as follows:
chr1 155743 N 15 <<<>>><>>>>><Gg
chr1 155744 N 15 <<<>>><>>>>><Tt
chr1 155745 N 15 <<<>>><>>>>><Aa
chr1 155746 N 15 <<<>>><>>>>><Cc
chr1 155747 N 15 <<cCCCcCCCCCcCc
chr1 155748 N 15 <<tTTTtTTTTTtTt
chr1 155749 N 15 <<gGGGgGGGGGgGg
chr1 155750 N 15 <<aAAAaAAAAAaAa
It's showing N because I did not use a reference index. However, my question is why there are < and > in the column for read bases? I'm thinking they might refer to reads that span exon-exon junctions. Has anyone else encountered them before?
Thanks.
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