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djhn75 / RNAEditor

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Annotation problem: All of my editing sites are in intergenic region #11

Closed WYSNI closed 7 years ago

WYSNI commented 7 years ago

Hi,

I have a problem with the annotation. In fact, all of my editing sites are annotated in intergenic region. I have used bedtools intersect with the RefSeq file in reference and many positions found with RNAEditor are on coding regions.

I don't know if it's a problem with the gtf file used for the annotation but i have follow explanations on the "Download annotations" item except i use the last version of GRCH37.

Do you have any ideas of what appends?

Best,

WYSNI

djhn75 commented 7 years ago

Hi, it could be possible that there is a problem with the GTF file, because if no overlaps can be found the regions is assigned as intergenic.

Could you please send me log file from the run and the firat 200 Lines of the gtf file?

Best regards David

Am 02.05.2017 um 11:56 schrieb WYSNI:

Hi,

I have a problem with the annotation. In fact, all of my editing sites are annotated in intergenic region. I have used bedtools intersect with the RefSeq file in reference and many positions found with RNAEditor are on coding regions.

I don't know if it's a problem with the gtf file used for the annotation but i have follow explanations on the "Download annotations" item except i use the last version of GRCH37.

Do you have any ideas of what appends?

Best,

WYSNI

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-- David John Institute of Cardiovascular Regeneration Theodor-Stern-Kai 7 D-60590 Frankfurt am Main +49 69 6301 87952 John@med.uni-frankfurt.de

WYSNI commented 7 years ago

Thanks for the quick reply,

when I make: print(self.genesByChromosome[chromosome]) on the file Genome.py for the verification of the loop line 286, I obtain [ ] thats why all is considered like intergenic.

files.zip

Do you see a problem?

Best WYSNI

WYSNI commented 7 years ago

Hi David, Have you see the problem?

Best, WYSNI

djhn75 commented 7 years ago

Dear Wysni, no i havent found any problems in your GTF file. But the software seems to have any problems assembling genes from your gtf file. I will have a closer look at this problem soon. But so far you should use the annotations provided on the website: http://rnaeditor.uni-frankfurt.de/download.php

I am sorry i cant give a better solution so far. Best David