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sagnikbanerjee15 / Finder

A fully automated gene annotator from RNA-Seq expression data
MIT License
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Not stranded annotation on the final GTF file #51

Open vccarneiro opened 2 years ago

vccarneiro commented 2 years ago

Dear Sagnik, I am trying to use the annotation file within CellRanger (10X genomics) but it doesn't accept non-stranded exons. In which step are they being considered, and how can I obtain this information to prepare a useful .gtf ? Thanks for your assistance! Best wishes,

Vitor.

sagnikbanerjee15 commented 2 years ago

Hello Vitor,

Thank you for reporting this. I will take care of this in the next release. For the time being, you can convert the non-stranded exons to the positive strand by using the following command:

cat <gtf filename>|awk -F"\t" '{if($7 == ".") {$7="+"}}1' > <new gtf filename>

PS: I did not test the command. So please let me know if anything is broken.

Thank you.