Question: How to map reads onto human hg38 gene body regions instead of whole genome?
0
gravatar for kindle.ama98
13 days ago by
kindle.ama980 wrote:

Hi there, I am thinking of mapping reads onto gene bodies to make it less strict for off-target identification. Wondering if there's any file there already, or I have to extract certain regions manually. Thanks!

alignment genome • 251 views
ADD COMMENTlink modified 12 days ago by jordi.planells330 • written 13 days ago by kindle.ama980
1
gravatar for jordi.planells
12 days ago by
jordi.planells330 wrote:

I would get the fasta file of the human transcripts and map it against it. You can get the RefSeq annotation from here. Then you can build an index with your favorite aligner and align against it.
Other option would be to extract the genes from a gtf annotation and use bedtools getfasta to get the fasta file from the desired intervals.

ADD COMMENTlink written 12 days ago by jordi.planells330
0
gravatar for karl.stamm
13 days ago by
karl.stamm3.9k
United States
karl.stamm3.9k wrote:

Can't say if it's a good idea or not, but the way I would do that is to mask the genome reference. Just hack up your genome reference to have a bunch of NNNN in the intergenic regions.

Or use a transcriptome mapper like STAR/RSEM directly, and forego the genome mapping.

ADD COMMENTlink written 13 days ago by karl.stamm3.9k
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: 2076 users visited in the last hour
_