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Old 01-09-2013, 10:15 PM   #1
Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default TSS for encode data


i am new to chip-seq data analysis and right now i need to develop heatmaps to compare my data with the histone encode data (H3K4me3 and K27me3)

where do i get the TSS annotation files to compare?

Is there any good tool or software that compares the data between them

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Old 01-09-2013, 11:58 PM   #2
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Location: Bioinformatics Institute, SPb

Join Date: Jul 2012
Posts: 151

I'm not sure what are you asking exactly, but

you can get RefSeq annotation from USCS genome browser:

then you can use PeakAnnotator to see how your chip-seq data aligns with respect to RefSeq TSS
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Old 01-10-2013, 12:22 AM   #3
Location: philadelphia

Join Date: Aug 2012
Posts: 13

i need to develop a heatmap to compare my chipseq data with the encode tss data

for example like the image on the top of this page

i want to compare my data with H3K4ME3 and H3K27me3

for TSS this should i follow this steps

Go to the Tables section of UCSC (
Set each field to the following values:
Clade: Mammal
Genome: human
Assembly: hg19
Group: Genes and Gene Prediction Tracks
Track: RefSeq Genes
Table: refGene
Output format: BED - Bed Extensible Data
Click on Get output
On the next screen select Upstream by and set its value to 1
Click on Get BED

thank you
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