cds from IGV

Question

[eulalia.belloc]

Hi,

I would like to obtain the cds sequence from a gene that is not anotated in xenopus, but that I can find it in igv. I can see the sequence but I don't know how to obtain a FASTA format file of the cds.

thanks!

[h.mon]

What do you mean by "find it in IGV"? You can see it in the gene track (botton of IGV window) when you load the Xenopus genome on IGV? Or did you annotate by other means and load this custom annotation on IGV?

Answer 1

[GenoMax]

If you know the coordinates in the form of chrom start stop (BED format) then you can use samtools faidx (or pyfaidx or bedtools getfasta, search for those solutions here on Biostars) to retrieve the sequence you need from the genome sequence file.

samtools faidx reference.fasta
samtools faidx reference.fasta chr_ID:1-108

Answer 2

[lieven.sterck]

You could also use a different genome (track) visualization software such as GenomeView or Artemis or such which are specifically developed of annotating and thus offer easy and efficient ways to add/remove and get sequences for certain genes. But can be launch form the web so not local install needed.