Twobittofa download and install link?

Question

[Azhar]

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

[Rohit]

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.

Answer 1

[Kevin Blighe]

Last edited: September 27th, 2020 (while the washing machine spins the clothes)

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Dear Azhar,

You can download twobittofa from here:

• http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ (linux)
• http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/ (Mac)

To use it, first make it executable:

chmod 744 twoBitToFa

Then execute it like this:

./twoBitToFa hg38.2bit hg38.fasta

[foxdie]

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

[Kevin Blighe]

You appear to have downloaded the incorrect file (?). It should be just called twoBitToFa and is an executable.

Are you using Windows?

[miniyad8100]

i am also facing the same problem. i have downloaded twoBitToFa file. can anyone help me out ?

[Quentin M]

Try :

 ./twoBitToFa hg38.2bit hg38.fa

[miniyad8100]

it worked for me.

thank you so much

[Kevin Blighe]

Thanks Quentin. I edited the original post to reflect this.