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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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uTAR-aTAR read alignment ratio #18

Open Prakrithi-P opened 3 weeks ago

Prakrithi-P commented 3 weeks ago

Hi ! Thanks for the amazing pipeline! I remember reading before, but couldn't find the details now, so here I am. What is the number in the TAR read before _0 or after the strand? Is it the number of reads mapping to that region? I tried calculating it from the BAM but it din't add up to that number. Also I need to calculate the alignment ratio of uTARs and aTARs , but the intermediate bam files (*merged.bam and combined.bam) have been deleted so I can't directly calculate the read alignement ratio for those. Was wondering if I could use the numbers on the TAR IDs to calculate this.

Thanks and regards, Prakrithi

fw262 commented 2 weeks ago

Hi Prakrithi, so the number before the "_0" should be the strand-specific coverage based on the output of a "bedtools coverage" command. Please refer to https://github.com/fw262/TAR-scRNA-seq/blob/master/from_fastqs/README.md for more information.

Best, Michael