Question: Impact of RNAseq read length on non-reference genome alignment
gravatar for rependo
8 weeks ago by
rependo10 wrote:

Hi all,

I'm trying to get a sense for whether or not read length has an impact on alignment success when mapping to a non-reference/congener genome. I'm conducting a large, multi-species RNAseq experiment and we have an annotated genome for one focal species in the study; the plan is to align reads for multiple congeners to this reference. In designing the experiment, I've come to the question of whether or not to go with PE50 reads (cost effective) or PE100/150. The increased cost of longer reads might be justified if they improve the likelihood of unique mapping, but I'm having a hard time finding papers that address this specific question.

Any input would be greatly appreciated.

Edit: changed a word

rna-seq alignment • 103 views
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by rependo10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1615 users visited in the last hour