Question: Question chip enrichment
0
gravatar for kanwarjag
2.9 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

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 • 1.1k views
ADD COMMENTlink modified 2.9 years ago by Devon Ryan94k • written 2.9 years ago by kanwarjag1.0k
1
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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.

ADD COMMENTlink written 2.9 years ago by Devon Ryan94k

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

ADD REPLYlink written 2.9 years ago by kanwarjag1.0k

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

ADD REPLYlink written 2.9 years ago by Devon Ryan94k

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

ADD REPLYlink written 2.9 years ago by kanwarjag1.0k

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

ADD REPLYlink written 2.9 years ago by Devon Ryan94k

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

Here is the GTF file

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by kanwarjag1.0k

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

ADD REPLYlink written 2.9 years ago by Devon Ryan94k

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.

ADD REPLYlink written 2.9 years ago by kanwarjag1.0k

As an example, the GTF file from gencode

ADD REPLYlink written 2.9 years ago by Devon Ryan94k

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
ADD REPLYlink written 22 months ago by jbalberge100

Another reason not to use UCSC.

ADD REPLYlink written 22 months ago by Devon Ryan94k
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