Reference FASTA file for sequencing use

ashkot · 04-28-2015, 10:12 AM

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 · 04-28-2015, 10:29 AM

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 · 04-28-2015, 10:44 AM

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 · 04-28-2015, 11:05 AM

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 · 04-28-2015, 12:39 PM

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 · 04-28-2015, 06:17 PM

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

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04-28-2015, 10:12 AM	#1
ashkot Member Location: Cupertino, CA Join Date: Nov 2011 Posts: 59	Reference FASTA file for sequencing use 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.

04-28-2015, 10:29 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	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

04-28-2015, 10:44 AM	#3
ashkot Member Location: Cupertino, CA Join Date: Nov 2011 Posts: 59	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.

04-28-2015, 11:05 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	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.

04-28-2015, 12:39 PM	#5
ashkot Member Location: Cupertino, CA Join Date: Nov 2011 Posts: 59	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?

04-28-2015, 06:17 PM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	You could manually change the fasta headers to suite your purposes and remake the indexes.