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noush-joglekar / biccn_tilgner_scisorseq

Code for the BRAIN Initiative Cell Census Network (BICCN) - RF1 Tilgner
MIT License
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Isoquant results to AllInfo file #1

Closed biozhangzhou closed 6 months ago

biozhangzhou commented 6 months ago

Hello,

I didn't find the codes for processing the isoquant results into the extended annotation file and the AllInfo file. Can you share it with me?

Zhou

noush-joglekar commented 6 months ago

Hi Zhou,

The extended annotation file was made by just collating the lines containing "nic" i.e., "novel in catalog" transcripts from the "transcript_models.gtf" file onto the gencode annotation.

Converting the isoquant output to the all-info format can be done using the function "correctedBed2AllInfo" in scisorseqr. See ?scisorseqr::correctedBed2AllInfo for help

biozhangzhou commented 6 months ago

Thanks for the quick response.