iosonofabio
commented
5 years ago Hi Alice,
You can make up a GTF file or modify the htseq-count script, both ways will work.
Cheers Fabio
On Thu, Mar 7, 2019, at 14:37, MoutonAlice wrote:
Dear Simon, I have been asked to count the reads out of a customized bed files with around 900 coordinates. These coordinates do not always specifically match a gene id on my gtf file so I wanted to count the reads per coordinates. Reading the documentation, it seems that it is possible to customize the python script but before starting this, I want to be ure that it would be possible to do. I can't find a lot of information on this. Maybe I can convert my bed to gtf and it will work. Would you have some suggestions? Many thanks, Best regards Alice
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/simon-anders/htseq/issues/73, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJSAPtLmiwrFQN3SW5XWaSJQ2Q_HS7Hks5vUZScgaJpZM4bkQeJ.
Dear Simon, I have been asked to count the reads out of a customized bed files with around 900 coordinates. These coordinates do not always specifically match a gene id on my gtf file so I wanted to count the reads per coordinates. Reading the documentation, it seems that it is possible to customize the python script but before starting this, I want to be ure that it would be possible to do. I can't find a lot of information on this. Maybe I can convert my bed to gtf and it will work. Would you have some suggestions? Many thanks, Best regards Alice