Best software to map lncRNAs?
1
0
Entering edit mode
4.8 years ago

I have a fasta file with about 5800 lncRNAs found on F. vesca and I would like to map them in a reference genome. Which software should I employ? I don't know if HISAT or STAR could work with sequences of that length.

lncRNA mapping • 932 views
ADD COMMENT
2
Entering edit mode
4.8 years ago

I would suggest using minimap2 or GMAP for this task since both can do spliced alignment of long reads/fragments. Even if the reads are not entirely incorrect you should get nice results. Those tools also work with error-prone nanopore and Pacbio transcriptome sequencing.

ADD COMMENT

Login before adding your answer.

Traffic: 2474 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6