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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
56 stars 9 forks source link

how to discard more than one chromosomes with parameter -d #28

Closed ShuangHe33 closed 5 years ago

ShuangHe33 commented 5 years ago

Hi, I want to exclude chrY and chrM in the input bam file, I tried to use parameter "-d chrY_chrM" , it seemed that it was not the appropriate format.

Thank you in advance!

endrebak commented 5 years ago

It uses regular regexes. -d «(chrM|chrY)» should work.

You can play around with regexes here:

https://rubular.com/

Endre

On Sunday, August 4, 2019, ShuangHe33 notifications@github.com wrote:

Hi, I want to exclude chrY and chrM in the input bam file, I tried to use parameter "-d chrY_chrM" , it seemed that it was not the appropriate format.

Thank you in advance!

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endrebak commented 5 years ago

https://rubular.com/r/CsPzEkIjAPoga4

Feel free to ask more questions if something is unclear :)

ShuangHe33 commented 5 years ago

https://rubular.com/r/CsPzEkIjAPoga4

Feel free to ask more questions if something is unclear :)

Thank you ! I have another question : is the peak 1-based or 0-based?

endrebak commented 5 years ago

0-based :)

On Tuesday, August 6, 2019, ShuangHe33 notifications@github.com wrote:

https://rubular.com/r/CsPzEkIjAPoga4

Feel free to ask more questions if something is unclear :)

Thank you ! I have another question : is the peak 1-based or 0-based?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/epic2/issues/28?email_source=notifications&email_token=AEHURUQTT32RNFA4IMSKUBDQDDSXJA5CNFSM4IJE4UM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3TVVNI#issuecomment-518478517, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHURUV5F7DEPEHTGMRDTU3QDDSXJANCNFSM4IJE4UMQ .