Question: Extract MAF regions (transcripts) using GTF of exons
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gravatar for AidanQuinn
2.8 years ago by
AidanQuinn20
United States
AidanQuinn20 wrote:

Hello,

I am interested in extracting multiple species alignment for a subset of species included in the UCSC multiz100way whole genome alignment. My GTF file contains exons, but ultimately I'd like to stitch together the full length transcripts and obtain FASTA formatted alignments for each transcript.

Does anyone know which tools I can use to do this?

My current plan is to use PHAST tools like msa_split to obtain the MAF of just there regions and species of interest but then I'm not sure how to recover transcripts. Any thoughts or suggestions are welcome!

Thanks!

ADD COMMENTlink modified 2.8 years ago by natasha.sernova3.4k • written 2.8 years ago by AidanQuinn20
0
gravatar for natasha.sernova
2.8 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

There was a post about it:

Is There An Easy Way To Read The Maf Files On The Ucsc Website?

maf-parse utilities:

http://compgen.cshl.edu/phast/help-pages/maf_parse.txt

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by natasha.sernova3.4k
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