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erhard-lab / price

Improved Ribo-seq enables identification of cryptic translation events
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gedi -e Price -percond flag #6

Closed TamaraO closed 6 years ago

TamaraO commented 6 years ago

Hi Florian,

What does -percond flag mean for Price pipeline? It appears when I run multiple samples. What are the alternatives?

gedi -t /Ribo-seq/Price -e Price -reads /Ribo-seq/Price/./parameters/parameters.cit -genomic human_g1k_v37 -prefix /Ribo-seq/Price/./parameters/price/parameters -plot -percond -D

It's not in the help gedi -e Price -h.

Thank you,

Tamara

florianerhard commented 6 years ago

Hi Tamara,

gedi -e Price -h only tells you about mandatory parameters, try gedi -e Price -hh!

The -percond flag makes Price to estimate a codon model for each individual sample instead of a single model for the pooled samples. This should lead to more accurate mapping of reads to codons in most cases, so the pipeline uses that by default.

Florian