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TobiTekath / DTUrtle

Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
https://tobitekath.github.io/DTUrtle
GNU General Public License v3.0
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matrix of transcript counts #6

Closed yoavhadas closed 2 years ago

yoavhadas commented 2 years ago

Hello, Is it possible to import a matrix of transcript counts as txt or csv file instead of raw data?

Thanks Yoav

TobiTekath commented 2 years ago

Hi @yoavhadas ,

if you have a matrix file of counts, you can import it into R and directly plug it into the run_deseq2() or run_drimseq() functions.

Pease note that your data will not be scaled or normalized in any way by this approach though.

If you have a raw count file per sample, you could try the import_counts() function with type="none" and specify the columns with the data manually. Then an appropriate scaling should be applied.

Best, Tobi

yoavhadas commented 2 years ago

Thank you Tobi I will give it a try.

Yoav

yoavhadas commented 1 year ago

Hello again, In my csv file, I have barcodes as columns and transcripts as rows:

TranscriptID,CCGCAGTCAGGACTCA,TCATACCACTTGAGTT,TGCGCGTTAATTACCA,AAGTAGAGTACTAAGT Transcript1,0,0,0,0 Transcript2,0,0,0,0 Transcript3,0,0,3.93,0

I can import it to R using read.csv("transcript_matrix.csv"); however, I am not sure what you mean by: "specify the columns with the data manually."

Any help will be appreciated. Thanks Yoav.