Question: How to combine and make .fai for reference genome from chromosome-specific fasta sequences
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gravatar for soosus
4.8 years ago by
soosus10
United States
soosus10 wrote:

I have downloaded compressed versions of .fastas for Drosophila melanogaster from ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Drosophila_melanogaster/chromosomes/.They are chromosome specific and I need to combine them into one .fasta with an adjoining .fai (which from what I gather I can use samtools to compile) in order to use the files as a reference genome on the Ion Proton system for next generation sequencing. Any suggestions?

reference fai fasta genome • 2.2k views
ADD COMMENTlink modified 4.8 years ago by Ashutosh Pandey11k • written 4.8 years ago by soosus10
0
gravatar for Ashutosh Pandey
4.8 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Search for UNIX cat function online and see how it is used to concatenate multiple files into one file.

Samtools can be used to create .fai file from fasta file. Check the manual for samtools here: http://samtools.sourceforge.net/samtools.shtml

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Ashutosh Pandey11k

Here's my problem. I'm not sure which files to concatenate. There are Het and non-Het versions of the fastas for each chromosome found here ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Drosophila_melanogaster/chromosomes/

ADD REPLYlink written 4.8 years ago by soosus10

Check this post for your question: How To Decide Whether To Keep: Het, U And Extra For Mapping Drosophila Genome

ADD REPLYlink written 4.8 years ago by Ashutosh Pandey11k
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