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Bed file error #156
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Your input dm6.ncbi*bed file is corrupted. All coordinates in bed are always listed such that the start < end, also for - strand genes. This needs to be fixed. Afterwards, you can do this check with UCSC kent tools |
Thanks a lot! I got a new bed file and still get errors, I understand the last error about the not allowed characters but I don't understand the other ones since the bed file passed the previous checks.
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I believe the | chars are not allowed. The others are warnings of transcripts which do not have a proper reading frame and will be ignored. |
Thanks, Now with 'normal' IDs it stills trows some of the warnings as before and it moves a bit forward but stalls later.
But those IDs do exist in the 2bit file. I even converted the 2bit back to fasta and the headers are there
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You have JAPIVC010000807.1 and not JAPIVC010000807 in the 2bit file |
But in theory that's not true because:
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All scaffold names have to match, otherwise the method does not know what is what. |
Thanks! |
I am a bit confused. The TOGA error indicates that either the bed or the chain file have JAPIVC010000001 while the 2bit has JAPIVC010000001.1 We always strip the .1 from scaffold name when we load a genome, as there is no reason to have .1 attached. Could you pls try to remove the .1 from all files that TOGA gets? |
Hi @LliliansCalvo I suspect the chain file has chromosome/scaffold names without .1... |
Hi I am trying to run TOGA, so far u successfully ran the first part to make the alignement.
However whenever I try to run TOGA I get an error related to the bed file that I don't really know how to troubleshoot.
Thanks!
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