polyA/polyT/lowcomplexity region realignments for single ended reads

[avilella]

Hi,

I would like to ask about ABRA realignment of single-fragment (non-paired) reads around regions where there is a poly-A or poly-T or low complexity region where bowtie2/bwamem are unable to properly align the reads one-by-one but there is a possibility of improving the alignment when looking at the pileup in the region.

Would ABRA be able to work on regions like that even when the reads are single-fragment?

[mozack]

Hi, We've seen cases where calls at short homopolymer runs or short tandem repeats are improved even in single end data. However, as the total repeat length starts to approach the read length, ABRA will have less or no impact.

[avilella]

I have run it for a small set of regions, but so far it seems ABRA prints
out the same alignments than the input bam. Any parameters I should play
with?

On Mon, Feb 22, 2016 at 3:35 PM, Lisle Mose notifications@github.com
wrote:

Hi, We've seen cases where calls at short homopolymer runs or short tandem
repeats are improved even in single end data. However, as the total repeat
length starts to approach the read length, ABRA will have less or no impact.

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[mozack]

Difficult to say. Are you able to share a BAM snippet?