How to combine and make .fai for reference genome from chromosome-specific fasta sequences · Biostar

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How to combine and make .fai for reference genome from chromosome-specific fasta sequences

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 genome fasta fai

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updated 12.2 years ago by Ashutosh Pandey

• written 12.2 years ago by soosus •

1 answer

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.

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updated 6.8 years ago by Ram

• written 12.2 years ago by Ashutosh Pandey

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/

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written 12.2 years ago by soosus •

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

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written 12.2 years ago by Ashutosh Pandey

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