all interactions filtered out - error

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Issue #26 new
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I used HiC-Pro to generate BAM files and then the bam2chicago.sh script to get the chinput file. I then ran the runChicago.R wrapper and I get:

I'm getting the following output: Processing input...

Read 0.0% of 7227576 rows Read 16.9% of 7227576 rows Read 33.2% of 7227576 rows Read 49.9% of 7227576 rows Read 67.0% of 7227576 rows Read 83.4% of 7227576 rows Read 7227576 rows and 4 (of 4) columns from 0.214 GB file in 00:00:09 minFragLen = 150 maxFragLen = 40000 Filtered out 1110 interactions involving other ends < minFragLen or > maxFragLen. minNPerBait = 250 Filtered out 5210 baits with < minNPerBait reads.

Error in readSample(inputFiles, cd) : All interactions have been filtered out. Execution halted

Any assistance is much appreciated! Thanks Lea

Comments (1)

  1. Mikhail Spivakov

    It seems like 5210 baits are filtered out due to their having < minNPerBait reads. Could it be that this is all the baits you have? If so try adjusting that minNPerBait parameter. Please see ?defaultSettings and ?modifySettings for details.

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