Question: Prediction of TSS from tuxedo pipeline
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gravatar for bioinfo_ga
2.3 years ago by
bioinfo_ga20
bioinfo_ga20 wrote:

I have 22Million (150*2) human transcriptome reads. I have performed reference alignment using tuxedo pipeline (Tophat followed by Cufflinks).I need to calculate transcription start site (TSS) in my aligned transcripts and how to calculate position of TSS with respect to proximal and distant promoter.

tss rna-seq tuxedo • 555 views
ADD COMMENTlink modified 2.3 years ago by jnoble33320 • written 2.3 years ago by bioinfo_ga20
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gravatar for jnoble333
2.3 years ago by
jnoble33320
jnoble33320 wrote:

I think in the case of a + strand transcript your TSS would be the leftmost position in exon 1 of the transcripts in the gtf file generated by cufflinks.

ADD COMMENTlink written 2.3 years ago by jnoble33320
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