How to I map paired end reads on BLAT?

[reyy14]

Hello, I'm new to this forum.

I just have a question on how to map paired end reads on BLAT.

I have an SRA file, which were splitted into 2 separate fasta file for each end and I'm stuck on mapping them on BLAT.

How do I need to go about this?

Any help would be appreciated.

Thank you!

[GenoMax]

Since blat is not PE aware you would essentially need to map them individually. Any particular reason you are using blat and not one of the NGS aligners that know about PE data?

[reyy14]

I am trying to follow along a paper that I am currently reading, https://www.ncbi.nlm.nih.gov/pubmed/25635456

[GenoMax]

I see. Looks like they only mapped R1 with blat and then checked for the presence of a linker barcode in R2 and then used bowtie to map.

[reyy14]

Alright got it. Thanks so much for the help GenoMax!

[reyy14]

Oh by the way, are there any tools that would help me remove the linker barcode? Or would I have to code it myself?

[GenoMax]

If it is the same for all reads (and in same spot) then you could use bbduk.sh from BBMap suite using literal=linker_sequence_here option (or cut N bases from front/end of read etc). There is a thread for bbduk here. Search for it.