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

Question

[soosus]

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?

Answer 1

[Ashutosh Pandey]

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.

[soosus]

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/

[Ashutosh Pandey]

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