Interpreation of RSEQC read_distribution.py results

richardallenfriedman · 11-08-2020, 02:44 PM

Dear Seqanswers List,

Here is my ouput from read_distribution.py from RSEQC run from Galaxy

Total Reads 54875279
Total Tags 58170116
Total Assigned Tags 54031503
=====================================================================
Group Total_bases Tag_count Tags/Kb
CDS_Exons 39184887 10217883 260.76
5'UTR_Exons 37214570 10963357 294.60
3'UTR_Exons 58010731 4386101 75.61
Introns 1539911688 6018229 3.91
TSS_up_1kb 24518972 906468 36.97
TSS_up_5kb 110212503 4956374 44.97
TSS_up_10kb 201827137 13004223 64.43
TES_down_1kb 27333233 59583 2.18
TES_down_5kb 118264548 3689226 31.19
TES_down_10kb 210002921 9441710 44.96

My questions:
Where does rRNA fit in this picture?
What about other transcripts other than mRNA such as pseudogenes?

Thanks and best wishes,
Rich
Richard Friedman,
Columbia University

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11-08-2020, 02:44 PM	#1
richardallenfriedman Junior Member Location: Brooklyn NY, USA Join Date: Nov 2020 Posts: 1	Interpreation of RSEQC read_distribution.py results Dear Seqanswers List, Here is my ouput from read_distribution.py from RSEQC run from Galaxy Total Reads 54875279 Total Tags 58170116 Total Assigned Tags 54031503 ===================================================================== Group Total_bases Tag_count Tags/Kb CDS_Exons 39184887 10217883 260.76 5'UTR_Exons 37214570 10963357 294.60 3'UTR_Exons 58010731 4386101 75.61 Introns 1539911688 6018229 3.91 TSS_up_1kb 24518972 906468 36.97 TSS_up_5kb 110212503 4956374 44.97 TSS_up_10kb 201827137 13004223 64.43 TES_down_1kb 27333233 59583 2.18 TES_down_5kb 118264548 3689226 31.19 TES_down_10kb 210002921 9441710 44.96 My questions: Where does rRNA fit in this picture? What about other transcripts other than mRNA such as pseudogenes? Thanks and best wishes, Rich Richard Friedman, Columbia University