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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
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[BUG] #146

Closed fork16 closed 1 week ago

fork16 commented 9 months ago

Description

I have two sample to detect orfs. One is done but another gets following bug.

What I Did


ribotricer detect-orfs --bam ${file} --ribotricer_index ${ribotricer_index_tsv} --prefix ${file/bam/} --report_all --phase_score_cutoff 0
Sep 14 10:25:03 ..... started ribotricer detect-orfs
Sep 14 10:25:03 ... started parsing ribotricer index file
Sep 14 10:25:07 ... started inferring experimental design                                                                               
Sep 14 10:25:07 ... started reading bam file
Sep 14 10:25:10 ... started plotting read length distribution                                                                           
Sep 14 10:25:10 ... started calculating metagene profiles. This may take a long time...

Sep 14 10:25:10 ... started plotting metagene profiles
Sep 14 10:25:10 ... started inferring P-site offsets
WARNING: no periodic read length found... using cutoff 0.0

The difference between the two files is not significant, but read counts of successful one is more than another one. image image

Is this an error caused by the read counts?

saketkc commented 1 week ago

This is not a bug. Ribotricer could not find evidence for periodicity in any of the read lengths. You can lower the periodicity threshold and see if that helps.