Question: samtools faidx redirection
2
gravatar for cristian
4.1 years ago by
cristian250
cristian250 wrote:

Dear Community, I am using 'samtools faidx' to index a fasta file. samtools faidx output/genome/ref/seq/celegans.fa However, this command creates a 'celegans.fai' file in the same folder as the fasta file. Is there a way to specify in which folder to store the index file? Samtools help can be found here: http://www.htslib.org/doc/samtools.html Thanks.

ADD COMMENTlink modified 4.1 years ago by Pierre Lindenbaum131k • written 4.1 years ago by cristian250
1
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:
ln -s /path/to.fasta x.fa && samtools faidx x.fa && rm x.fa

or

samtools faidx /path/to.fasta x.fa && mv /path/to.fasta.fai x.fa.fai
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Pierre Lindenbaum131k

There is a small typo. faix should be faidx.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by genomax92k

fixed thanks

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k

OK thank you very much.

ADD REPLYlink written 4.1 years ago by cristian250
1

it worked ? flags this question as answered please.

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k
2

Have a feeling people don't understand use "checkmark" to flag as answered. Perhaps there should be a word description there as well.

ADD REPLYlink written 4.1 years ago by genomax92k
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