TATA box enrichments around the TSS of mouse genes

[Sam]

Hi there,

After looking at the gallery of deepTools plots, I came across the TATA box enrichment heatmap which I would like to reproduce for my data.

Unfortunately, I can't seem to get the bigWig file containing the psem scores.

• signal file: bigWig file of TATA psem scores

Has anyone got any experience of trying to do this/has the file?

Best regards,

Sam

[Thomas Manke]

Dear Sam,
We did not keep the bigwig file for this illustration. But I have
attached the psem file for TBP, so you can generate the bigwig file for
your favorite genome using the TRAP tool:
https://github.com/maxplanck-ie/TRAP
There are various options for window size etc, but the basic command
would be

> utilities/trap.sh -s genome.fa -m TATA.psem -g genome.fa.fai -d outdir

Since TRAP predates bigWig, you'll need UCSCtools for the conversion
from bedgraph.

Feel free to contact me directly if you have problems with it.
Best wishes,
Thomas

On 02.09.19 17:23, Sam wrote:
> Hi there,
>
>
> After looking at the gallery of deepTools plots, I came across the
> TATA box enrichment heatmap which I would like to reproduce for my data.
>
> Unfortunately, I can't seem to get the bigWig file containing the psem
> scores.
>

> * /signal file/: bigWig file of TATA psem scores

>
> Has anyone got any experience of trying to do this/has the file?
>
>
> Best regards,
>
> Sam

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[s...@splitty.org]

Dear Thomas,

Thanks for your quick reply!

That's brilliant, thank you for supplying me with this.

With regards to the command line to run, I've tried running it but sadly comes up with:

../utilities/trap.sh -s GRCm38_sm.fa -m TATA.psem -g GRCm38_sm.fa.fai -d ../../DeepTools

require environment variable $TRAPPATH

(this is when running it from the bin folder).

Any idea what the problem might be? Or will i have to manually change the environment variable.

Best regards,

Sam

[s...@splitty.org]

Dear Thomas,

I've managed to get it operating - i've installed TRAP and ucsctools (so i can get wigToBigWig) and have set the environment variables $TRAPPATH and $UCSCPATH to the locations required.

However, it runs for about a second, creates all the directories ("trapTest" - the output directory i created, inside which is "bedgraph" - contains an empty GRCm38_sm_M00471.bedgraph file, "bigwig" which is empty and "matrices" containing the file "matrix_00000" which contains the text below):

>M00471 /name='V$TBP_01' /type='psem' /strand='+' /size='8' /gc='0.5' /pseudocount='1' /lambda='0.7' /pseudocount='1'  /AC='M00471' /consensus='TATAAATW'

2.97063 2.65185 1.66164 0

0       5.07907 2.2992  2.10844

5.53029 5.53029 5.53029 0

0       5.53029 5.53029 5.53029

0       5.53029 5.53029 5.53029

0       4.31489 3.00591 3.73566

3.13889 3.13889 2.33944 0

0       2.11658 2.11658 0.209434

The directory also contains "log" which contains:

############################

Tue Sep  3 23:53:51 BST 2019

# split matrix file TATA.psem into individual chunks: trapTest/matrices

/scratch/c.c1866917/TRAP/bin/ANNOTATE_v3.05 -s GRCm38_sm.fa --psem trapTest/matrices/matrix_00000 -g 0.5 -R 50 | /scratch/c.c1866917/TRAP/utilities/trap2bg.pl -norm log | sort -k1,1 -k2,2g > trapTest/bedgraph/GRCm38_sm_M00471.bedgraph; /scratch/c.c1866917/ucsctools/wigToBigWig trapTest/bedgraph/GRCm38_sm_M00471.bedgraph GRCm38_sm.fa.fai trapTest/bigwig/GRCm38_sm_M00471.bw

For reference, the command line i use is:

../TRAP/utilities/trap.sh -s GRCm38_sm.fa -m TATA.psem -g GRCm38_sm.fa.fai -d trapTest

Any idea what's going wrong? Thanks again!

Best regards,

Sam

> an email to deep...@googlegroups.com
> <mailto:deep...@googlegroups.com>.

[Thomas Manke]

Dear Sam,
Everything looks ok from my side. Please be aware that your job may continue to run in background.
Depending on your resources, the whole process (TRAP-->normalization --> bedgraph-->bigwig) can take up to 15min+.
If it still fails, please send me the output from

> /scratch/c.c1866917/TRAP/bin/ANNOTATE_v3.05 -s GRCm38_sm.fa --psem trapTest/matrices/matrix_00000 -g 0.5 -R 50 | head

Best wishes,
Thomas
PS> you might try a smaller fasta file for initial testing
PPS> I suggest we take this off the deeptools list - since this is TRAP specific.

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-- 
Dr. Thomas Manke
Head of Bioinformatics
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, 79108 Freiburg, Germany
Tel. +49-761-5108 738
Fax  +49-761-5108 80738