[Genome] is there a fast BED2seq tool?

[Hiram Clawson]

Good Morning Stein:

Surprisingly enough, I do not see a stand alone tool in the source
tree to do a reverse complement.  There is a function for it of course
in the libraries, but no command line access to it.

Good idea for such a feature in twoBitToFa.

--Hiram

On 2006 Nov 22, , at 12:12 AM, Stein Aerts wrote:

> Hi Rachel, Hiram,
>
> Thanks, this all works very well.
> I'm left with one detail however: the strand in the BED file is not 
> taken into account when using this:
>
> awk '{printf "%s:%d-%d\n", $1, $2, $3}' file.bed \
>        | twoBitToFa hg18.2bit output.fa -seqList=stdin
>
>
> So I presume it returns only + strand sequences. I could reverse 
> complement the - strand features using a bioperl script, but perhaps 
> it's possible with the ucsc tools in one go?
>
> Stein
>
>
>
> Hiram Clawson wrote:
>>
>> You can create a dm2.2bit file from the fasta sequence in:
>>     ftp://hgdownload.cse.ucsc.edu/goldenPath/dm2/bigZips/
>> with the program: faToTwoBit
>>
>> --Hiram
>>
>>> On Tue, 21 Nov 2006, Stein Aerts wrote:
>>>
>>>> Hi Rachel,
>>>> Thank you for the quick reply - this seems indeed the solution for 
>>>> me.
>>>>
>>>> I could find a hg18.2bit file in hg18/nib but I particularly need 
>>>> the fly
>>>> species, and I couldn't find any 2bit file in
>>>> ftp://hgdownload.cse.ucsc.edu/gbdb/dm2/nib. Could it be somewhere 
>>>> else
>>>> perhaps?
>>>>
>>>> Many thanks again for all the help,
>>>> Stein Aerts