Masking repetitive sequences ...can I then map using BWA?

Question

[ab.tsubaki]

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

[Devon Ryan]

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?

[ab.tsubaki]

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?

[Devon Ryan]

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

[ab.tsubaki]

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