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lavenderca / TSScall

TSScall identifies transcription start sites (TSSs) from Start-seq data (Nechaev et al. Science, 2010). Operating both with and without a reference annotation, TSScall allows for rapid annotation of TSSs across an entire genome.
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Can TSScall be used to call PolII reads clusters using proseq data? #7

Closed cxue closed 6 years ago

cxue commented 6 years ago

Hi, Lavenderca, Because TSScall provide the information of START-seq reads clusters, I am wondering whether it can be used to extend to call gro-/pro-seq reads clusters from gro-/proseq-data. If yes, it would be extend the usage of TSScall. Is it right?

best

Cheng Xue

lavenderca commented 6 years ago

Hi, Cheng,

We developed TSScall to work specifically with Start-seq data. While the algorithm used by TSScall could likely be applied to other techniques, we haven't tested this. If applied to other methods, like GRO-seq or PRO-seq, I would take care in evaluating the results.

Best,

Andy

cxue commented 6 years ago

Hi, Andy, Thank you for your response. In my understanding, TSScall calls the cluster of START-seq peak reads, and then get the uTSS and annotated TSS. In gro-seq/pro-seq, TSScall calls the cluster of PolII reads, which is similar to STAR-seq with the similar input. The difference is that START-seq reads focus on TSS while gro-seq/pro-seq reads show the location of PolII. I just hope that TSScall can provide some peak cluster of PolII. Can I do it using TSScall? or could you recommend some revision processes or other software to do this. Thanks!!

best
Cheng
lavenderca commented 6 years ago

I would personally recommend Homer. It uses a pretty straightforward method for calling TSSs from GRO-seq data that may work for PRO-seq. You could also try groHMM, which is part of Bioconductor.

Andy

cxue commented 6 years ago

Thank you!!