identifyDistal3UTR gives a blank output file?

[Peter Combs]

Hi Dr Ye,
I'm trying to use APAtrap on some fly data that I have, but I suspect that I have a subtly wrong annotation file(?), because the output file ref.novel.utr.bed is totally blank:

$ head -n 5 melsim/Reference/ucsc_annotation.bed
dmel_4  251355  266500  CG1674-RB       0       +       252579  266389  0       11      166,43,570,81,81,81,291,85,320,115,695, 0,1205,1549,3535,4134,5665,6539,9584,12536,12904,14450,
dmel_4  252055  266500  CG1674-RC       0       +       252579  266389  0       9       198,43,81,81,291,85,320,115,695,        0,505,2835,4965,5839,8884,11836,12204,13750,
dmel_4  252108  265205  CG1674-RA       0       +       252579  264217  0       12      122,43,570,81,81,291,117,85,138,219,483,162,    0,452,796,2782,4912,5786,7639,8831,9213,10978,11783,12935,
dmel_4  380577  395610  CG1710-RC       0       +       381316  393018  0       13      24,420,310,212,189,146,1074,1089,238,155,267,364,2735,  0,635,2352,2719,2994,3542,3916,5722,9555,9858,11139,11861,12298,
dmel_4  380587  395610  CG1710-RB       0       +       381316  393018  0       13      19,420,310,212,189,146,1074,1089,238,155,267,364,2735,  0,625,2342,2709,2984,3532,3906,5712,9545,9848,11129,11851,12288,
$ head -n 5 melsim/merged/ref.coverage.bedgraph
dmel_2L 9107    9125    1
dmel_2L 9125    9130    5
dmel_2L 9130    9131    6
dmel_2L 9131    9137    8
dmel_2L 9137    9138    9
$ APAtrap/identifyDistal3UTR -i melsim/merged/ref.coverage.bedgraph -m melsim/Reference/ucsc_annotation.bed -o melsim/merged/ref.novel.utr.bed
# Output snipped for brevity
$ wc -l melsim/merged/ref.novel.utr.bed
0 melsim/merged/ref.novel.utr.bed

Any guidance you have on where I might have gone wrong would be appreciated! I'm happy to attach full versions of either the annotation or coverage bedgraph if that would be more helpful.

Cheers,
Peter

[Congting Ye]

Hi Peter,

It would be great that you could send me the annotation and coverage files for figuring out the problem. My email address is yec@xmu.edu.cn.

Congting Ye

[Peter Combs]

In case someone else comes across this issue, the problem seems to be that I had an underscore in all of my chromosome identifiers. Conting replied to an email and said "Any annotation with a chromosome id containing underline symbol '_' will be discarded for further analysis in our design, which is used to filter out some special annotations. "

The code is now running, and while I haven't evaluated the output yet, I'm optimistic.