Question about TES and TSS plotting and heat map matrix

[kanw...@gmail.com]

I have two questions-

1. 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. I used bed file of TSS but how it will map TES, Do I supply second file if TES, then how should I take into account variation in transcript length.

2. I used bam compare and compute matrix and heat mapper to generate a heat map, similar to example  @ http://deeptools.readthedocs.org/en/latest/content/tools/plotHeatmap.html

I can get the average matrix for profile plot but can I get the matrix for plotting heat map using other resources in order to better control the image. 

Thanks

Kanwar

[Friederike Dündar]

Dear Kanwar,

regarding your 1st question:

All you need to supply is a BED file with the entire gene lengths, deepTools will identify TSS and TES by using the start and end coordinates noted in the 2nd and 3rd column. Then choose computeMatrix's scale-regions mode and define

--beforeRegionStartLength 10000 --afterRegionStartLength 10000

Also see https://github.com/fidelram/deepTools/wiki/Visualizations

 for more details.

Regarding your 2nd question:
You can export all the data that computeMatrix and heatmapper/plotHeatmap generate.
I am not 100% sure which data type you are after, but hopefully the explanations here: https://github.com/fidelram/deepTools/wiki/All-command-line-options#heatmapper

will help.

Let me know if anything is still unclear.

Best,

Friederike

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[zhuli...@gmail.com]

Dear Friederike,

For the deeptools computeMatrix to generate intermediate files for plotProfile, I am wondering whether it will tell genes in positive strand and negative? When I use it to draw metagene plots based on ATAC seq data based on all human genes, ideally there would be peaks only in the TSS, but the result turned out there are also peaks around the TES, and that was because of the genes in negative strand. Is there any parameters handling this which I have found yet?

Thank you very much in advance!
Lina

[Devon Ryan]

Hi Lina,

If the file you give to computeMatrix indicates the strands
appropriately (i.e., the file is in BED or GTF format) then
computeMatrix will automatically handle strand information and reverse
genes/transcripts on the - strand.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

[zhuli...@gmail.com]

Yes, I figured it out just now and found I input them in a wrong format so deepTools can not make use of the strand information.

Thank you so much for your quick reply!