Samtools faidx problem

Question

[maxime.policarpo]

Hello everyone,

I am interested in a sequence ranging from 111614 to 111868 in a fasta sequence (scaffold sequence)

I am trying to use samtools faidx to tkae this sequence but it doesn't work and keep returning me :

[fai_fetch] Warning - Reference 111-555 not found in FASTA file, returning empty sequence

After seeing some other users with the same problems, i tried to change the header name for it to contain no space (like ">scaffoldX") but it still doesn't work

Here is the exact command I type (my fasta file only contain the sequence of my scaffold) :

samtools faidx scaffold.fasta 111614-111868

Thanks a lot for your help.

[maxime.policarpo]

If someone know an other way to simply extract a sequence from pos X to Y in a fasta file, i am interested ! Thanks ^^

Answer 1

[cmdcolin]

Shouldn't it be "samtools faidx scaffold.fasta scaffoldX:111614-111868"?

[maxime.policarpo]

It worked !! Thanks a lot ! I feel so stupid now

[WouterDeCoster]

The same issue probably explains why bedtools didn't work.

I have moved the comment of cmdcolin to an answer so you can accept it to mark this thread as solved.

Answer 2

[WouterDeCoster]

This sounds like a job for bedtools getfasta.

[maxime.policarpo]

Sounds awesome, going to check it, thanks !

[maxime.policarpo]

It doesn't seems to work better ...

bedtools getfasta -fi scaffold.fasta -bed test.bed > result_test

Result : nothing ...

[WouterDeCoster]

I have no idea how the chromosome identifier of your fasta file looks like, and how you formatted your bed file. As such you are making it rather hard to troubleshoot.