Question: Best software to map lncRNAs?
0
gravatar for Francisco Muñoz
17 months ago by
Francisco Muñoz 0 wrote:

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 • 473 views
ADD COMMENTlink modified 17 months ago by WouterDeCoster40k • written 17 months ago by Francisco Muñoz 0
2
gravatar for WouterDeCoster
17 months ago by
Belgium
WouterDeCoster40k wrote:

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 COMMENTlink written 17 months ago by WouterDeCoster40k
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: 926 users visited in the last hour