I have two gff files, one containing transcript sequences, another containing TranscriptionStartSites (TSS).
Now I would like to compare these two gff's and for each transcript sequence find the closest upstream TSS.
Is there a Tool that can do this?
I tried closestbed, but every time a TSS is present inside my transcript sequence it will report this one in stead of looking further. Is there maybe a way to disable reports of overlapping features?
I also looked into the galaxy-flanking_features, from the description this seems to do what I want but it is no longer available on our systems...
Anyone have any tips? Before I start writing my own script...
Now I would like to compare these two gff's and for each transcript sequence find the closest upstream TSS.
Is there a Tool that can do this?
I tried closestbed, but every time a TSS is present inside my transcript sequence it will report this one in stead of looking further. Is there maybe a way to disable reports of overlapping features?
I also looked into the galaxy-flanking_features, from the description this seems to do what I want but it is no longer available on our systems...
Anyone have any tips? Before I start writing my own script...
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