how can I remove the unwanted fasta sequences?

Question

[Yingzi Zhang]

Dear all, I got simulation whole-genome nanopore sequences (reference hg19) like this:

>chr1_113769058_aligned_6_F_18_10356_19
ACGGGC...
>chr1_183621434_aligned_7_F_24_5152_2
TCCTCCGC...
>chr1_55334860_aligned_8_F_27_8746_17
ACGCCT...

I want to remove all the sequences covered the gene BBIP1, that is within chr10_112658488-112678694. So I think I need to remove all the fasta sequences with >chr10_ and following between 112658488 and 112678694. Can anyone help me how to realize it please? Thank you very very much..

Yingzi

Answer 1

[Matteo Schiavinato]

I guess the only reliable way you can do this is to map these sequences against the BBIP1 gene sequence, and then keep those that don't map.