Question chip enrichment

Ihave simple chip seq input and enriched data. I want to generate figs 1 C or 2 C of http://www.nature.com/nature/journal/v473/n7347/pdf/nature10066.pdf and am sure I can use deeptools. In deep tools from where we take TSS and TES file? Is there any other tool that can give me thes figures.

chip-seq deeptools

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updated 9.3 years ago by Devon Ryan

• written 9.3 years ago by kanwarjag

1 answer

You can just download a GTF file from Ensembl or UCSC and use that. computeMatrix will figure out where the TSS and TES for each transcript is then.

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written 9.3 years ago by Devon Ryan

Hi Devon, BTW you know that deeptools Galaxy version is not working properly, It hide files and than show error in running. It is happening from last month or so., Now I am trying galaxy main instance. Thanks

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written 9.3 years ago by kanwarjag

I wasn't aware of that, I'll have to take a look on Monday when I'm back in the office.

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written 9.3 years ago by Devon Ryan

I used GTF file of hg19 and got following error:

Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/bin/computeMatrix", line 11, in <module> main(args) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/computeMatrix.py", line 414, in main hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/heatmapper.py", line 247, in computeMatrix keepExons=keepExons) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptools/mapReduce.py", line 85, in mapReduce bed_interval_tree = GTF(bedFile, defaultGroup=defaultGroup, transcriptID=transcriptID, exonID=exonID, transcript_id_designator=transcript_id_designator, keepExons=keepExons) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptoolsintervals/parse.py", line 588, in __init__ self.parseGTF(fp, line) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptoolsintervals/parse.py", line 503, in parseGTF self.parseGTFexon(cols) File "/galaxy/main/deps/_conda/envs/mulled-v1-0fa290085c742a3ffee6a142d1fce47c178e1c289ff6f0c66023b506f3377842/lib/python2.7/site-packages/deeptoolsintervals/parse.py", line 439, in parseGTFexon if name not in self.exons[self.labelIdx]: IndexError: list index out of range

Here are few first lines of GTF file:

chr1 unknown exon 11874 12227 . + . gene_id "DDX11L1"; transcript_id "NR_046018_1"; gene_name "DDX11L1"; tss_id "TSS14523"; chr1 unknown exon 12613 12721 . + . gene_id "DDX11L1"; transcript_id "NR_046018_1"; gene_name "DDX11L1"; tss_id "TSS14523"; chr1 unknown exon 13221 14408 . + . gene_id "DDX11L1"; transcript_id "NR_046018_1"; gene_name "DDX11L1"; tss_id "TSS14523"; chr1 unknown exon 14362 14829 . - . gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359"; chr1 unknown exon 14970 15038 . - . gene_id "WASH7P"; transcript_id "NR_024540"; gene_name "WASH7P"; tss_id "TSS7359";

Any suggestion

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written 9.3 years ago by kanwarjag

Can you post a link to the GTF file you used?

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written 9.3 years ago by Devon Ryan

https://www.dropbox.com/s/9wkxj2mp2dyg8mp/hg19_genes.gtf?dl=0

Here is the GTF file

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written 9.3 years ago by kanwarjag

Your GTF file is missing all of its transcript and gene entries. You can find properly formatted files at UCSC, Ensembl, and Gencode.

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written 9.3 years ago by Devon Ryan

Is there a format that is compatible with deeptools, Could you please point me to either a previously downloadable file or few lines of formatted file.

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written 9.3 years ago by kanwarjag

As an example, the GTF file from gencode

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written 9.3 years ago by Devon Ryan

It seems that Gencode / RefSeq annotation files downloaded from UCSC in GTF format don't contain transcript and gene entries. I got the same error with gtf files downloaded on UCSC. Problem solved by downloading gtf files from Gencode instead.

> library(data.table)
> hg38.gtf <- data.table(fread("Downloads/hg38_RefSeq_UCSC.gtf"))
> table(hg38.gtf$V3)

    CDS        exon start_codon  stop_codon 
 564992      719285       56477       56417

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written 8.3 years ago by jbalberge

Another reason not to use UCSC.

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written 8.3 years ago by Devon Ryan