Masking repetitive sequences ...can I then map using BWA?
0
0
Entering edit mode
7.8 years ago
ab.tsubaki ▴ 50

Hi there

In need of help please!

I'm masking the repetitive regions in my wheat sequencing data using RepeatMasker. This generates a .masked file. Next I want to map or compare this masked file to other genome sequences but BWA uses fastq if I remember correctly. How can I convert the .masked file to a useable format? Or can it be used as-is???

Appreciate any comments, suggestions or previous experience :-)

Anandi

next-gen blast • 2.9k views
ADD COMMENT
0
Entering edit mode

Do you have to use BWA? It's intended for short reads, not whole genome comparisons. Why don't you just use a tool designed to compare genomes?

ADD REPLY
0
Entering edit mode

Well, I'm not QUITE comparing a whole genome. My contigs are quite short and that's what I'll be mapping first.

Any advice on other mapping programs will be appreciated? I know BWA and Bowtie and I don't think either of them makes mention of .masked files?

ADD REPLY
0
Entering edit mode

The .masked file is just a fasta file, at least that's my recollection.

ADD REPLY
0
Entering edit mode

Thanks! I looked at the output from RepeatMasker and saw that it's a fasta file just now! Clever me!

ADD REPLY

Login before adding your answer.

Traffic: 2269 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