Question: Creating genome alignment
0
gravatar for dec986
9 months ago by
dec986130
United States
dec986130 wrote:

Hello,

I am confused about the difference between GRCh37.p13.genome.fa (767 MB, http://www.gencodegenes.org/releases/19.html) and GRCh37.primary_assembly.genome.fa (830 MB http://www.gencodegenes.org/releases/27lift37.html) which is lifted from Gencode release 27. I want to use the most recent version of GRCh37, with the most corrections/updates/etc. I can't use GRCh38 because of alt loci making accurate quantification difficult.

I can see pluses and minuses for each choice. which genome should I be using for STAR genome alignments?

Perhaps there is a version of GRCh37.p13.genome.fa which is lifted or related to release 27?

rna-seq star • 345 views
ADD COMMENTlink modified 9 months ago by lshepard130 • written 9 months ago by dec986130

Heng Li has a blog post on which human genome to use.

ADD REPLYlink written 9 months ago by genomax58k
0
gravatar for lshepard
9 months ago by
lshepard130
United States
lshepard130 wrote:

From the Gencode website:

"Primary assembly: Nucleotide sequence of the GRCh38 (or GRCh37 if you want that) primary genome assembly (chromosomes and scaffolds) The sequence region names are the same as in the GTF/GFF3 files"

The larger file contains all regions including assembly patches and haplotypes. Normally, most people choose primary assembly. But to note, using the latest version (GRCh38) shouldn't really give you any issues with STAR and downstream analysis.

ADD COMMENTlink modified 9 months ago • written 9 months ago by lshepard130
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: 1710 users visited in the last hour