search

AAlhendi1707 / countToFPKM

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
GNU General Public License v3.0
61 stars 15 forks source link

Using The [CollectInsertSizeMetrics(Picard)] tool #12

Closed Sanataniitb closed 2 years ago

Sanataniitb commented 2 years ago

This tool requires input BAM/SAM file for finding out the mean fragment length. Where as I have only the count matrix file. Is there any way to find the mean fragment length if I only have the count matrix file.

xiaowenchenjax commented 2 years ago

I have the same issues. look forward to your reply. thanks.

AAlhendi1707 commented 2 years ago

Hi both, You need average fragment lenght to convert count matrix to FPKM. If you are using read count data from publicly available datasets such as https://www.ebi.ac.uk/arrayexpress, or GEO expression datasets, then the insert size is mentioned in the metadata section of the experiment. Hope it helps!