Quantcast
Channel: Post Feed
Viewing all articles
Browse latest Browse all 3231

Aligning Paired-End Reads In Single-End Mode

$
0
0

Hello,

I have a question on how to align paired-end reads.

In cases of very large fastq files, which make aligners like TopHat crash in a server with limited memory in RAM, I have seen people align one pair mate at a time, to prevent TopHat from crashing. I cann't come up with an argument against doing this, but am tempted to reason that one should always align paired-end reads in "paired-end mode".

My question is: How are downstream analyses affected if one aligns paired-end reads one pair mate at a time, setting BWA or Bowtie/TopHat to single-end mode?

Thanks, G.


Viewing all articles
Browse latest Browse all 3231

Trending Articles