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adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
https://www.cbu.uib.no/valen/
GNU General Public License v3.0
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Gene/transcript IDs annotation support? #42

Closed sunsetyerin closed 1 year ago

sunsetyerin commented 1 year ago

Hi @adnaniazi, I was able to generate output table. But wonder how can I get the gene or transcript IDs.

adnaniazi commented 1 year ago

Hi @sunsetyerin,

There is an undocumented function in tailfindr that you can use for that purpose. It is called annotate_tails.

Use it like this

df <- annotate_tails(sam_file,
                           tails_csv_file,
                           output_file)

where sam_file is the alignment of your reads with your reference in SAM format. tails_csv_file is the output of the tailfindr containing tail lengths. output_file is the full filepath for the file in which the new result should be stored.