pileup file symbols "<" and ">"

[geraldgsw]

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.

[krobison]

Yes, those are places which are between exon junctions (intronic sequence). The specification document could use this to be added.

[geraldgsw]

Thank you! I thought so from comparing different positions, but was not sure.

[Benjamin Vincent]

Can you identify read bases from these sequences?

Hello,
I have a similar pileup file, and I am trying to calculate information content at each position in the alignment. Is it possible to tell from the '<' and '>' characters what the specific read bases are? Sorry if I've missed something completely obvious and thanks for your help.