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fw262 / TAR-scRNA-seq

scRNA-seq analysis beyond gene annotations using transcriptionally active regions (TARs) generated from sequence alignment data
GNU General Public License v3.0
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Is there any chance running this pipeline totally without 'REFGTF'? #17

Closed buhanfeng closed 2 years ago

buhanfeng commented 2 years ago

Hi all,

I'm dealing with a strange species which has no gtf at all. Is there any chance running this pipeline totally without 'REFGTF'?

fw262 commented 2 years ago

Hello,

The pipeline does not explicitly perform the analysis without a reference GTF file.

Fortunately, there is a file created called "TAR_reads.bed.gz" in rule "rule calcHMMbed" of the Snakefile which contains all the peaks in your dataset. You can actually use the regions defined in "TAR_reads.bed.gz" file as your annotations or genome reference. You can easily convert this bedfile to a .gtf or .refFlat format (refer to convertRefFlatToGTF.R script for help) for downstream analysis.

Best, Michael

buhanfeng commented 2 years ago

Hi Michael,

Your advice is very helpful, I use a dummy gtf file to run the pipeline, and obtain TAR_reads.bed.gz .

Thanks for your help.