hi I want to build index for bowtie2 , i downloaded genome file from bowtie2 link , but these genome file are .bt2 form . I think i have to covert them into fasta formate and concatenate and then build index. For converting .bt2 files into fa formate which software is used ?
i think twobittofa is used but i did not get a link to download install and use can some body forward me this link?
thanks Regards
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written
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Azhar •
Last edited: September 27th, 2020 (while the washing machine spins the clothes)
Dear Azhar,
You can download twobittofa from here:
To use it, first make it executable:
chmod 744 twoBitToFa
Then execute it like this:
./twoBitToFa hg38.2bit hg38.fasta
twobittofa hg38.2bit hg38.fasta
I could not get it to just run like this. Does this have something to do with exporting the path or something (new to this, sorry)?
This is what I get:
[~/Desktop]
>>>>>>>>>> chmod 744 twoBitToFa.dms
[~/Desktop]
>>>>>>>>>> twobittofa mm10.2bit mm10.fa
-bash: twobittofa: command not found
You appear to have downloaded the incorrect file (?). It should be just called twoBitToFa and is an executable.
Are you using Windows?
i am also facing the same problem. i have downloaded twoBitToFa file. can anyone help me out ?
Try :
./twoBitToFa hg38.2bit hg38.fa
it worked for me.
thank you so much
Thanks Quentin. I edited the original post to reflect this.
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It's easier to download the genome from UCSC or ensembl and construct the index yourself. Also, bowtie already provides some pre-indexed genomes. If you already have the indexed files, then you can start with the alignment already. Also, 2bit format has nothing to do with the bt2 format of bowtie.