Question: combining fasta files
4
gravatar for br.tania
23 months ago by
br.tania40
br.tania40 wrote:

I have downloaded the assembly fasta files for all chromosomes for an organism from NCBI. Now I want to map my unique data (WGS) to the genome. How to combine the chromosome-wise fasta files to give a fasta file for the whole genome? This needs to be done to run BWA, right?

alignment • 1.8k views
ADD COMMENTlink modified 14 months ago by manishagupta2930 • written 23 months ago by br.tania40

Thanks a lot. That was useful.

ADD REPLYlink written 22 months ago by br.tania40

How to combine the chromosome-wise fasta files to give a fasta file for the whole genome? what was the answer to this question?

ADD REPLYlink written 14 months ago by manishagupta2930

This question has been asked multiple times. You can simply do cat chr*.fa > genome.fa. (replace chr* with whatever names you have). If the names follow no pattern then do cat file1.fa file2.fa ... file_last.fa > genome.fa.

ADD REPLYlink written 14 months ago by genomax62k

Which software is recommended for this task?

ADD REPLYlink written 14 months ago by manishagupta2930

genomax posted the command you would use in your command line.

ADD REPLYlink written 14 months ago by WouterDeCoster36k

I m using Windows 10, where i have to put these commands?

ADD REPLYlink written 14 months ago by manishagupta2930

Do you have Ubuntu bash for Windows 10 installed? Otherwise you may be able to do copy file1 file2 > final in a windows command prompt. You can't get much done with plain Windows 10 in terms of NGS data analysis (unless you use one of the commercial software packages).

ADD REPLYlink written 14 months ago by genomax62k
4
gravatar for Devon Ryan
23 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

cat *.fa > genome.fa

You'll need to index that with bwa or whatever aligner you plan to use then.

ADD COMMENTlink written 23 months ago by Devon Ryan88k
1

As far as I remember bwa index -p myindex *.fa would also work.

ADD REPLYlink written 23 months ago by WouterDeCoster36k
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