computeMatrix parameters as shown in Galaxy video

[carolni...@gmail.com]

I downloaded the command line version of deeptools, and then tried to replicate the video tutorial shown on Galaxy. However, I cannot replicate the heatmap exactly. My reads are all shifted to the right of the TSS, unlike the nice evenly centered plot I get running Galaxy (see attached files).

I have narrowed down the error to the computeMatrix function. What are the command line parameters for computeMatrix command as shown in the video tutorial? I am using the following commands but they dont give me the same heatmap:

computeMatrix reference-point -R GRCh37_promoters.bed --referencePoint=center -S H3K4Me1_log2ratio.bw H3K4Me3_log2ratio.bw -b 3000 -a 3000 -out GRCh37_promoters_matrix

Any advice would be greatly appreciated.

Thank you,

Carol

[Fidel Ramirez]

Hi,

The two images that you sent correspond to:

 * the one with the reads shifted left is for command line version

 * the one with the reads not shifted is the galaxy version.

Both heatmaps use the same bigwig files.

Is this correct?

-fidel

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Fidel Ramirez

[Fidel Ramirez]

The labels of the images where not easy to spot, now I see that what I wrote is correct.

In my opinion the command line version, with the uneven peaks, is the correct one. The nucleosome free region is quite clear and appears as an straight line. And I have seen this same result in some publications.

In the galaxy version, it appears as if the TSS is not properly defined. The nucleosome free region is no longer a straight line. To me it seems that the promoters do not have strand information. Can you check that?

Best,

Fidel

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Fidel Ramirez

[obri...@tcd.ie]

Hi Fidel,

Thank you so much for your reply.

Yes, the promoter file does have strand information, it is the example file 'GRCh37_promoters.bed' provided in Galaxy. I used this same file for both heatmaps. I also used the same bamCompare files for both. I suspect there must just be one command different between the two in the computeMatrix function.

I'm glad to hear my command line plot looks okay - your observations make sense. I'm happy to continue my analysis on the command line now.