CHM13 PROseq Track Settings
CHM13 PROseq stranded with unique genome-wide kmer filtering   (All mRNA and EST tracks)

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Type of graph:
Track height: pixels (range: 11 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 127)
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Windowing function: Smoothing window:  pixels
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Graph configuration help
All subtracks:
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 PROseq default NEG  PROseq default NEG no kmer filtering   Schema 
 PROseq default POS  PROseq default POS no kmer filtering   Schema 
 PROseq k100 NEG  PROseq k100 NEG no kmer filtering   Schema 
 PROseq k100 POS  PROseq k100 POS no kmer filtering   Schema 
 PROseq k100-21mer NEG  PROseq k100 NEG 21mer filtering   Schema 
 PROseq k100-21mer POS  PROseq k100 POS 21mer filtering   Schema 
 PROseq k100-dual-21mer NEG  PROseq k100 NEG dual 21mer filtering   Schema 
 PROseq k100-dual-21mer POS  PROseq k100 POS dual 21mer filtering   Schema 


CHM13 PRO-seq (Precision Run-On sequencing) Bowtie2 alignments to CHM13v2.0 (minus chrY) and unique genome-wide 21mer filtering (stranded)

PRO-seq detects nascent transcription (including from non-coding) from RNA polymerases with nucleotide resolution at genome-scale.


The PRO-seq experiment was done on CHM13 cells (in duplicate, A and B) and sequenced from the 3' end for 75bp single-ended reads. Reads were adapter trimmed, quality filtered (-q 20), and length filtered (-m 20) with Cutadapt (v2.7). Trimmed reads were then reverse complemented since they were sequenced in the 3'-->5' direction. D. melanogaster spike-ins were removed with Bowtie2 (v2.3.5.1) and samtools view -f 4 (v1.9). Reads were then mapped with either Bowtie2 (v2.3.5.1) default or -k 100 (allowing up to 100 multi-mappers). Unique genome-wide 21mers were generated through Meryl ( The reads mapped with -k 100 were filtered with these unique genome-wide 21mers through one of two methods:

  1. Locus-specific unique genome-wide 21mer filtering (overlapSelect -overlapBases=21; UCSC tools (GenomeBrowser/20180626))
  2. Read- and locus-specific unique genome-wide 21mer filtering (, overlapSelect -overlapBases=21)

Display Conventions and Configuration

The tracks labeled as "neg" are negated for viewing.

Data access

Raw PRO-seq data filled under BioProject PRJNA559484

Release history

  1. CHM13v2.0 assembly (minus chrY)



For generation of unique genome-wide 21mers:

For the PRO-seq experimental, mapping, and filtering methods: