Question: Masking reference for RNA-seq alignments
0
gravatar for thjnant
5.0 years ago by
thjnant90
Germany
thjnant90 wrote:

Hi,

I have a general question about mapping RNA-seq data to the reference genome. I was wondering whether it matters if the reference genome is masked for repeats or not when mapping RNA-seq reads? if so, should it be hard mask or soft mask?

Thanks

rna-seq • 3.0k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 5.0 years ago by thjnant90
0
gravatar for Devon Ryan
5.0 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Most aligners don't care if bases are soft-masked and there's typically no point in hard-masking for aligning RNAseq datasets (though perhaps you have a non-standard dataset). If, for some reason, you need to avoid aligning to repeat regions then use a hard-masked genome.

ADD COMMENTlink written 5.0 years ago by Devon Ryan92k

Thanks for your reply. No, I have a standard RNA-seq dataset and although I have generated the masked genomes, I used the non-masked version for alignment because I thought it should not matter for RNA-seq data because they are coming from exons which I assume contains no long range repeats.

ADD REPLYlink written 5.0 years ago by thjnant90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1034 users visited in the last hour