search

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
159 stars 81 forks source link

annotate peaks produced by this pipeline #112

Closed llz-hiv closed 6 years ago

llz-hiv commented 6 years ago

Hi Jin,

The format of peak files produced by this pipeline seems are bigwig or BB, can I use these files directly for annotation of genomic feature? What I am using for annotation is Chipseeker, it seems that chipseeker prefer '.bed' as its input format.

Thanks!

akundaje commented 6 years ago

The peaks are in narrowPeak and bigbed format. Narrowpeak is an extended bed format. https://genome.ucsc.edu/FAQ/FAQformat.html#format12

On Tue, May 8, 2018, 8:36 AM llz-hiv notifications@github.com wrote:

Hi Jin,

The format of peak files produced by this pipeline seems are bigwig or BB, can I use these files directly for annotation of genomic feature? What I am using for annotation is Chipseeker, it seems that chipseeker prefer '.bed' as its input format.

Thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kundajelab/atac_dnase_pipelines/issues/112, or mute the thread https://github.com/notifications/unsubscribe-auth/AAI7Ea609Rg_T2R9_OSNv_zB7A-UkFjyks5twbuJgaJpZM4T234L .

llz-hiv commented 6 years ago

It works, thank you!