Reference FASTA file for sequencing use

[ashkot]

Hi all,
I downloaded FASTA files from NCBI and tried to use them in my sequencing pipeline. The issue is that within the FASTA file the sequences were represented using their genbank accession and due to this the genbank accession also appreared in the VCF file which is undesirable.

Is there a way to prepare a FASTA file so that chromosome number is used or rather is there a way to "prepare" a FASTA file for sequencing use?

Thank in advance.

[GenoMax]

What "genome" is this?

You can get pre-formatted sequence, annotation and index files for a number of common organisms at the iGenomes site: http://support.illumina.com/sequenci...e/igenome.html

[ashkot]

That site has only up to hg18 for human but if I wanted to use much older genome assemblies? And my work is for human genome analysis.

[GenoMax]

I would suggest that you get older data from from UCSC: http://hgdownload.soe.ucsc.edu/downloads.html#human Look for "chromFa.zip" files in the "Full Dataset" links.

[ashkot]

We did take those file and there is no issue with those files. There are some other old genomes which we require and that is the issue.

I am wondering if there is some code that can standardize sequence names across fasta file?

[GenoMax]

You could manually change the fasta headers to suite your purposes and remake the indexes.