Error in AnnotatePeaksFromGTF() about sierra

[rj-patrick]

Hi @pk43429,

Thanks for trying out Sierra. Can I just ask a clarifying question, the peak file you are using, is that from a set of merged peaks across multiple BAMs (generated using MergePeakCoordinates) or is it from a single run with the FindPeaks function only?

[pk43429]

Hi @reprobate,

It is from a single run with the FindPeaks function. I am testing the program on one bam file.

[rj-patrick]

Hi @pk43429,

We'll look into why this is occurring - in the meantime I've added an additional filter that will allow you to rerun FindPeaks without those peaks being included in the final output. Let me know if you have any more problems.

[pk43429]

Thank you @reprobate.

I tried the new version, but polyA_ID is now missing from the peak.table. Should I e-mail you a link to the files I am using?
head(peak.table)
`
Gene Chr Strand MaxPosition Fit.max.pos Fit.start Fit.end mu
1 TSPAN6 X -1 100636793 100636803 100635693 100636866 310.5894
2 TSPAN6 X -1 100629936 100632491 100629139 100637182 463.3069
3 TSPAN6 X -1 100633465 100633519 100632544 100635198 354.2600
4 TSPAN6 X -1 100629538 100629429 100628937 100629921 191.7233
5 TSPAN6 X -1 100636719 100636701 100636554 100636791 955.5231
6 DPM1 20 -1 50958456 50958483 50955276 50958555 327.8080
sigma k exon.intron
1 21.29481 3092.9806 non-juncs
2 320.55395 1406.2782 non-juncs
3 46.52637 1094.5792 non-juncs
4 164.41886 641.8294 non-juncs
5 49.14677 12504.8888 junctions
6 43.13418 7056.3381 non-juncs
exon.pos
1 (100635693,100635745)(100636793,100636866)
2 (100629139,100629985)(100630759,100630865)(100632485,100632567)(100633405,100633538)(100633931,100634028)(100635178,100635251)(100635558,100635745)(100636793,100637182)
3 (100632544,100632567)(100633405,100633538)(100633931,100634028)(100635178,100635198)
4
5
6 (50955276,50955284)(50958363,50958555)

`

[rj-patrick]

Hi @pk43429,

The polyA_ID column is added at the end, and the remaining data is written to file as it is generated, so the likely cause is that something has caused FindPeaks to stop before it completed. Can you check if there was an error message returned by FindPeaks?

I'm also happy to try running the program on the data you're using if you send me a link.

[rj-patrick]

Hi @pk43429, I'm going to close this issue if you have no more problems.