samtools faidx not finding my modified sequence

Question

[andrebolerbarros]

Hey everyone,

I want to add a customized sequence to the fasta file of my reference genome. So, I concatenated both files:

cat Homo_sapiens.GRCh38.dna.primary_assembly.fa Gene_mod.fa > HSapiens_Ensembl111mod.fa

In the Gene_mod.fa, the header of the sequence is similar to the ones found in the fasta:

>AddedSeq dna:scaffold scaffold:GRCh38:AddedSeq:1:2913:1 REF

Afterwards, to subset the file using samtools faidx for chromosome 3 and the AddedSeq, using the command:

samtools faidx HSapiens_Ensembl111mod.fa 3 AddedSeq >HSapiens.GRCh38_Chr3_AddedSeq.fa

it says it failed to retrieve AddedSeq.

Is there any problem with my code? I have used this fasta file for other purposes (like STAR) and it gave me no issues or problems.

Cheers

Answer 1

[ATpoint]

It is almost certainly all these whitespaces that mess things up. Replace them by a proper delimiter such as underscore in your fasta before concatenating the AddedSeq to the genome.

[andrebolerbarros]

I have removed all of that text and it solved the problem, thanks!

The structure of the header was similar when compared with the dna.primaryassembly.fa I got from Ensembl. In addition, when using this structure and a .gtf file to match, it seemed to worked fine...