How to use MSU7 rice genome as reference as there has fasta file format.
1
0
Entering edit mode
12 months ago
Mainul ▴ 10

I am working with Whole-genome sequence analysis. I have to use the MSU7 rice genome as a reference. Once I going to download reference seq from this site (http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/). I am not getting any fasta file format. there got gff and another file format that I am not familiar with. Anyone please help where I get MSU7 reference seq with the fast format. I am using the GTAK pipeline for the assembly. Thanks in advance.

Assembly genome alignment • 300 views
ADD COMMENT
0
Entering edit mode
12 months ago
ATpoint 49k

The README says:

all.con: complete genome sequence for each of the 12 pseudomolecules, the Syngenta pseudomolecule and the unanchored BAC pseudomolecule.

Try that and be sure to read documentation.

ADD COMMENT
0
Entering edit mode

all.con is a complete genome sequence but is it a sequence to use alignment on BWA. as BWA only supports .fa file.

ADD REPLY
1
Entering edit mode

It is fasta format. It is ready for use with bwa or any other aligner. It is indeed not common to name a file .con but there is no strict rule about this. This below is fasta format regardless of the suffix:

> name
sequence
ADD REPLY
0
Entering edit mode

Thanks, for your information.

ADD REPLY

Login before adding your answer.

Traffic: 2159 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