suggestion for hicAggregate and hicAverage

[fgualdr]

Hi,

for both functions would be really useful if strand informations stored in BED could be taken into account in order to make the aggregation and average strand aware. This would be extremely useful when for example plotting TSS to TES regions.

[LeilyR]

for know I would suggest you to generate a TSS or TES bed file from your original bed file. (one base length rows)

[fgualdr]

thanks for the quick reply.
My point is to make the mean/median or sum aggregation in order to have all on the "+" strand by transposing the sub matrix of features in the BED which are on the minus strand... don't know if my point is clearer.

[LeilyR]

I am not sure I understand you but why don't you make two bed files then , one with positive and the other with the negative strands, then run hicAggregate twice, once on each of them.

[fgualdr]

Thanks again,
yes that I could do. The point is if I then want to combine the two separate aggregations into one only by transposing the one obtained with "-" strand BED.
Thanks

[joachimwolff]

Hi @fgualdr,

sorry for the delayed reply. I have finally some time atm to fix bugs and implement new features. Can you explain to me what you mean with transposing the one obtained with "-" strand BED.?

Thanks a lot,

Joachim

[fgualdr]

Hi, thanks for the reply.
Maybe I explained myself wrongly.
What I was after was to generate aggregated/average strand aware so that the average contacts across all view point stored in the BED file could take into account the strands directly from the BED file.
In other wards to average the contacts after flipping those on the "-" strand.
I am doing this looking at contacts around TSSs and it would be nice to generate the plot so that the termination sites are all on the right hand side.
I know I can make two aggregation plot one for the "+" and one for the "-" but would be nice to have the tool out of the box dealing with the strand.

Thanks again for the nice tool.
Francesco

[joachimwolff]

Ah, I think I get what feature you want.

[joachimwolff]

I implemented it the following:

• hicAggreagateContacts:

  • Strand + / +: as it used to be
  • Strand + / - : flip values left to right: [[1,2,3], [4,5,6]] becomes [[3,2,1],[6,5,4]]
  • Strand - / + : flip values up/down: [[1,2,3], [4,5,6]] becomes [[4,5,6],[1,2,3]]
  • Strand - / - : compute transpose: [[1,2,3], [4,5,6]] becomes [[6,5,4],[3,2,1]]

• hicAverageRegions:

  • Strand + : as it used to be
  • Strand - : transpose

The changes are in the branch aggregate_average_strand_information. They can be activated with the parameter --considerStrandDirection. Would be great if you can give me feedback if it works as you intended.

Best,

Joachim