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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
28 stars 8 forks source link

About the length of reads #115

Closed lbwfff closed 2 years ago

lbwfff commented 2 years ago

Hi, saketkc I have a question, when using ribotricer to predict orfs, what is the interval of read lengths considered by ribotricer? Thanks， LeeLee

saketkc commented 2 years ago

It automatically determines the most informative read lengths to use (based on if the metagene distribution for a given read length exceeds the cutoff): https://github.com/smithlabcode/ribotricer/blob/master/ribotricer/detect_orfs.py#L360. The profiles are then merged by determine an appropriate offset that maximizes the cross-correlation.

You can override this behavior by providing a list of read lengths to use and their corresponding p-site offsets: https://github.com/smithlabcode/ribotricer/blob/003a0199f63e1554238b9206131134d4931e2cf1/ribotricer/cli.py#L139 https://github.com/smithlabcode/ribotricer/blob/003a0199f63e1554238b9206131134d4931e2cf1/ribotricer/cli.py#L153

Feel free to reopen if you have any other questions.

lbwfff commented 1 year ago

It automatically determines the most informative read lengths to use (based on if the metagene distribution for a given read length exceeds the cutoff): https://github.com/smithlabcode/ribotricer/blob/master/ribotricer/detect_orfs.py#L360. The profiles are then merged by determine an appropriate offset that maximizes the cross-correlation.

You can override this behavior by providing a list of read lengths to use and their corresponding p-site offsets:

https://github.com/smithlabcode/ribotricer/blob/003a0199f63e1554238b9206131134d4931e2cf1/ribotricer/cli.py#L139

https://github.com/smithlabcode/ribotricer/blob/003a0199f63e1554238b9206131134d4931e2cf1/ribotricer/cli.py#L153

Feel free to reopen if you have any other questions.

Hi, saketkc

I understand that Ribotricer will Assessing the Periodicity of Read Length, but will Ribotricer assess all the read length in the BAM file? Even if it is far greater than or less than 30bp.

Thanks, leelee

saketkc commented 1 year ago

Yes