Question: Help with Piranha bin size for BED files
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gravatar for anu014
4.3 years ago by
anu014180
India
anu014180 wrote:

I am using Piranha for Clip-seq analysis. I'm not having score column for my BED file. How much my 'bin-size/-b' should be? Can I take difference between 'start' & 'end' coordinates?

The Piranha manual says that : The response file (always the first argument, and required) may contain: Raw read locations, in which case Piranha will bin the reads for you. If you provide your input like this, you MUST set the bin size option, or Piranha will treat your input as being already binned. If Piranha is creating bins from raw reads, it will always start at the first index of each chromosome (i.e. index 1) and move at a step size equal to the bin size. Bins with no reads in them will not be retained. link : https://github.com/smithlabcode/piranha

Command used : ./piranha-1.2.1/bin/Piranha -b 43 -s ./G/SRR1690969.bed > piranha_peaks_output

My BED file looks like this :

chr1 630917 630960 . . + chr1 632324 632367 . . + chr1 632327 632370 . . + chr1 632328 632371 . . + chr1 632329 632372 . . + chr1 632331 632374 . . + chr1 632332 632375 . . + chr1 632333 632376 . . + chr1 632334 632377 . . + chr1 632336 632379 . . + chr1 632340 632383 . . + chr1 632342 632385 . . + chr1 632343 632386 . . + chr1 632344 632387 . . + chr1 632346 632389 . . +

Thank you in advance.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by anu014180

I have the same question. I get "ERROR: binning reads failed. Reason: size of required bins doesn't match size of actual bins" for the following command: ./Piranha -s -i 100 SMUG1.bed \ IgG.bed \ -o peaks.bed where 100 is bin size = read length.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by ofonov0
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