Query JASPAR data

Question

[Fussy89]

Hey, I would like to query data from the jaspar genereg database. I need information about the chromosomal location and the actual transcription factor to built sort of my own gtf file I tried to use the bioconductor package MotifDb but this does not work out. Any ideas? Thank you

Answer 1

[Denise CS]

Have you tried the Ensembl Regulatory build? Among other things, it's got the Transcript Factor Binding Site Annotation where the PWM are sourced from JASPAR. The file is available on the Ensembl FTP site and it's called MotifFeatures.gff.gz. The README me is also available.

Answer 2

[Fussy89]

Hey Thanks for your answer but I am not sure if it helps me... the file looks like this 1f8b 0800 2a67 cf56 0003 c4fd 4bcf 6dc9 7125 088e d9bf 22e7 0d08 fe7e 08a8 8182 6030 d1a0 2482 0a01 6a4e 0a21 6646 b600 .... So how is this telling me the chromosomal location and which tfbs it is? I would like to have something that looks like this chr start end score name strand eg. chr1 1 15 9.3 XYZ +

[Denise CS]

The file is compressed (gunzipped, gz extension). If you unzip it, you will be able to see meaningful numbers.