deeptools how to choose a bodylength

Question

[luckysardar171]

Hello, Anyone experiance with deeptools please suggest me how can I choose --regionBodyLength I know we have to provide int value but how to get this I am confused each gene body length vary so how can I do it suggest me I am new to deeptools

Thank you.

[Jianyu]

Which sub-command did you use?

[luckysardar171]

Jianyu I used computeMatrix scale-regions I want genebody enrichment plot

[Jianyu]

As far as I know, scale-region means the gene body will be rescaled to the same length, i.e., if you specify a 1kb body length, while the gene is only 100bp long, the gene body will be expanded 10 times (which means each base pair will be repeated 10 times); Oppositely, gene length exceeds the specified length will be "shrunken" to that length. So it seems to me, this option is used to control the ratios of upstream - gene body - downstream in the figure

[luckysardar171]

Jianyu Thank you for the clarification do you know which bed file format we have to give genewise or transcript wise I am bit confused in deeptool doc mentioned gene wise do you have any example file format please show few lines I am providing bedfile because some error is comming when I am using GTF file

[Jianyu]

Could you show us the error messages you got by using GTF file? I think the example provided in the doc is quite clear, you can check the full description of bed format here. Some tools like gtf2bed may help you deal with the format conversion

[luckysardar171]

here is my gtf and also providing subset of GTF

[Jianyu]

What's the error message deeptools gave you?

[luckysardar171]

Jianyu few lines of error some issues also present in github I feel something problem with the GTF file

"/home/.local/lib/python3.8/site-packages/deeptoolsintervals/parse.py", line 593, in __init__ self.parseGTF(fp, line) File "/home/.local/lib/python3.8/site-packages/deeptoolsintervals/parse.py", line 508, in parseGTF self.parseGTFexon(cols) File "/home/.local/lib/python3.8/site-packages/deeptoolsintervals/parse.py", line 444, in parseGTFexon if name not in self.exons[self.labelIdx]: IndexError: list index out of range

[Jianyu]

This message is not quite intuitive... But I did find a potential issue with the part of gtf file you showed above, where no transcript or gene entry can be seen... Try a gtf file with these entries see if that would work

[luckysardar171]

Jianyu, Okay Thank you what do you mean by no trascript or gene because gene_id and Transcript_id field is provided what is the issue I didnt get it...

[Jianyu]

chr1    3204562 3661579 NM_001011874 Xkr4   - 
chr1    4481008 4486494 NM_011441    Sox17  - 
chr1    4763278 4775807 NM_001177658 Mrpl15 -
chr1    4797973 4836816 NM_008866    Lypla1 +

I found this in deeptools doc

[luckysardar171]

Jianyu Yeah I have seen this format for clarification asking this is a gene start and end right not transript start and end, because of this I was confused which bed file I have to give gene or Trascript start and end