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AAlhendi1707 / countToFPKM

Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
GNU General Public License v3.0
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How to calculate meanFragmentLength #4

Closed excel9 closed 4 years ago

excel9 commented 4 years ago

Hello,

I am very new to bioinformatics and I am trying to use your Rcodes to calculate FPKM from a paired-end RNA seq count file. I am stuck at the use of CollectInsertSizeMetrics(Picard) tool to calculate meanFRagmentLength. I was wondering if you could provide a step-by-step guidance to using that tool. The rest of your instructions are very easy to understand from a standpoint of biologist who is very new to bioinformatics.

Thank you for your help!

AAlhendi1707 commented 4 years ago

Hi there,

Please find the answer in the below link https://github.com/AAlhendi1707/countToFPKM/issues/1 kind regards

mholtz2 commented 1 year ago

The issue you link to still does not give instructions on the inputs for CollectInsertSizeMetrics. I am having trouble understanding how to produce the appropriate input files. Please provide code or more clear instructions for this that a beginner can follow.