RNA-seq QC¶
1. read distribution¶
module load conda3
source activate /home/yli11/.conda/envs/rseqc
read_distribution.py -i test.markdup.uq.bam -r /home/yli11/Data/RSEQC_bed/hg19_RefSeq.bed
Output:
Total Reads 550
Total Tags 607
Total Assigned Tags 468
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Group Total_bases Tag_count Tags/Kb
CDS_Exons 34584069 184 0.01
5'UTR_Exons 7945567 107 0.01
3'UTR_Exons 27291196 52 0.00
Introns 955378898 91 0.00
TSS_up_1kb 19477091 0 0.00
TSS_up_5kb 88605716 4 0.00
TSS_up_10kb 161012560 20 0.00
TES_down_1kb 19913631 0 0.00
TES_down_5kb 85343516 4 0.00
TES_down_10kb 151518466 14 0.00
=====================================================================