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wdecoster / cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
MIT License
127 stars 11 forks source link

Reads length within specific regions #31

Closed Mannyari closed 3 months ago

Mannyari commented 3 months ago

Hi, could you consider adding an option to calculate statistics from one or more specific regions of a long-read sequencing dataset? Thank you in advance.

wdecoster commented 3 months ago

Hi,

cramino can read from stdin, so you could use samtools view to select a specific region from your alignment file, then pipe that into cramino. Would that work for you?

Best, Wouter

Mannyari commented 3 months ago

Hi Wouter,

Apologies for the late reply, but I managed to work on this only this morning. Yes, it worked! Thanks a lot, and great work with the tool.

Best, Arianna

Il giorno ven 26 lug 2024 alle ore 16:01 Wouter De Coster < @.***> ha scritto:

Hi,

cramino can read from stdin, so you could use samtools view to select a specific region from your alignment file, then pipe that into cramino. Would that work for you?

Best, Wouter

— Reply to this email directly, view it on GitHub https://github.com/wdecoster/cramino/issues/31#issuecomment-2252841462, or unsubscribe https://github.com/notifications/unsubscribe-auth/BEP5T2OSL6K24LYK3AFN5FDZOJJCZAVCNFSM6AAAAABLQP3RA2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJSHA2DCNBWGI . You are receiving this because you authored the thread.Message ID: @.***>

wdecoster commented 3 months ago

Thanks for the feedback! Please let me know if you have any other questions or suggestions.