Graphical map of TFBSs

0

Entering edit mode

2.5 years ago

arsala521 ▴ 30

Hi everyone,

I have a bed file showing binding sites of Su(H) transcription factor in extended gene regions of some D. melanogaster genes. I want to generate a graphical map showing these TFBSs across the length of these extended gene regions. I thought uploading the bed file on genome browser (Jbrowse) would generate this map but I didn't get anything on uploading the file as shown in tutorials. Is there any tool that can help me in generating this plot or is there some other way to use Jbrowse?

Thank you

Genome Jbrowse browser • 586 views

ADD COMMENT • link updated 2.5 years ago by cmdcolin ★ 3.8k • written 2.5 years ago by arsala521 ▴ 30

1

Entering edit mode

I'm a jbrowse developer, would be happy to help with jbrowse if interested. If you can describe the steps you took more I might be able to see more. YOu mentioned "I didn't get anything on uploading the file as shown in tutorials". If that means you have a track but nothing is visible on the track, then I would check if the chromosome names in your BED file match those in the reference sequence e.g. it should say "chr1" in both the BED file and the FASTA file

ADD REPLY • link 2.5 years ago by cmdcolin ★ 3.8k

Login before adding your answer.