.chinput does not show actual distance?

[Noboru Sakabe]

I'm failing to call interactions in my data set because all my probes are filtered out due to:

minFragLen = 150 maxFragLen = 40000
Filtered out 10123657 interactions involving other ends < minFragLen or > maxFragLen.
Error in FUN(X[[i]], ...) : All interactions have been filtered out.

I noticed that my .chinput file differs from your example. otherEndLen does not contain the length of the restriction fragment and distSign is not the distance between the centers of two fragments. I believe I may have created a bad probe map file but upon inspection I can't find out what's wrong.

##        samplename=all        bamname=all      baitmapfile=MboI.rmap      digestfile=probes-MboI_fragments.baitmap
baitID  otherEndID      N       otherEndLen     distSign
1000    392     1       100     832
1000    575355  1       100     441
100000  186347  1       100     362
1000005 1001242 1       100     1234

My .rmap file looks like this:

chr10   60106   61285   0
chr10   61285   62559   1
chr10   62559   62623   2
chr10   62623   62665   3
chr10   62665   63175   4

and my .baitmap looks like this:

chr10   94838   95131   77      TUBB8:NM_177987
chr10   95353   95607   81      TUBB8:NM_177987
chr10   179444  180358  294     ZMYND11:NM_006624
chr10   180358  183758  295     ZMYND11:NM_006624
chr10   183758  184113  296     ZMYND11:NM_006624

The ID's match in both files:

$ grep -w 1573 MboI.rmap probes-MboI_fragments.baitmap
MboI.rmap:chr10 735243  737247  1573
probes-MboI_fragments.baitmap:chr10 735243  737247  1573    DIP2C:NM_014974

I can make available all my input files, please, PM me if you want them. Thank you!

[Mikhail Spivakov]

Hi! I noticed that our .rmap files are 1-based, whereas yours is 0-based. I'm not sure this is what's causing the problem, but can you please check? If this turns out to be the case, we'll amend the docs to emphasise this point.

[Jonathan Cairns]

Hi,

From reading the .chinput header, have you got your .rmap and your .baitmap mixed up? (I'm also wondering if having samplename and bamname the same could be causing problems.)

Thanks,

Jonathan

[Noboru Sakabe]

Thanks for your help. Indeed, the files were swapped. bam2chicago.sh ran fine, without errors, so I thought there were no errors. Can I suggest implementing input checking and using getopts to read input options? It will be less confusing than entering options in the correct order.