samtools on centos

[vinaydu]

Dear all,

I have compiled and installed samtools as per the standard instructions given. When i tried to fetch sub region of a sequence it is giving the header only.

I am using the command

samtools faidx test.fasta

to create index file and then to fetch the sequence

samtools faidx test.fasta Wheat:5-15

This is just printing the fasta header and not fetching the sequence
>Wheat:5-15


Please help.....

[vinaydu]

Please reply guys.. Where I am committing mistake??? Please help..

[dpryan]

What happens if you type:

grep -A 1 Wheat test.fasta

[vinaydu]

Thanks

Thanks for the response.

Somehow samtools has started working fine automatically. I have not made any changes.

Thanks to establish such a nice forum...

[vinaydu]

In reply to Pryan,

It is giving the first line of the fasta file of Wheat header. Anyhow samtools has started working all fine on its own.

Thanks for your support.