Question chip enrichment

Question

[kanwarjag]

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.

Answer 1

[Devon Ryan]

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.

[kanwarjag]

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

[Devon Ryan]

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

[kanwarjag]

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

[Devon Ryan]

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

[kanwarjag]

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

Here is the GTF file

[Devon Ryan]

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

[kanwarjag]

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.

[Devon Ryan]

As an example, the GTF file from gencode

[jbalberge]

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

[Devon Ryan]

Another reason not to use UCSC.