User: eschang1

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eschang110
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Posts by eschang1

<prev • 7 results • page 1 of 1 • next >
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Mismatch between gene IDs in Map-SeqNum-ID.txt and HierarchicalGroups.orthoxml
... Hi there, Thanks so much for all of your help so far. I recently completed a successful OMA standalone run and am now digging into the results using the PyHam python package. One thing that I have noticed so far is that there seems to be a mismatch between the gene IDs as laid out by OMA in the Map ...
oma orthology pyham written 7 months ago by eschang110 • updated 7 months ago by adrian.altenhoff620
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Comment: C: OMA Phase 2 stuck in "reading all vs. all" stage for 24 hours
... Hello Adrian, I let my most recent OMA run just get killed due to the walltime limit (24 hours) to see if the buffers would indeed be flushed, and it looks like it died while doing a bunch of additivity checks, i.e. `VP check additivity: daphnia_pulex/04002 vs hydra_magnipapillata/19500 by orbice ...
written 8 months ago by eschang110
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Comment: C: OMA Phase 2 stuck in "reading all vs. all" stage for 24 hours
... Thank you for the tip! ...
written 8 months ago by eschang110
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OMA Phase 2 stuck in "reading all vs. all" stage for 24 hours
... Hi there, I have just completed the all vs. all phase of the OMA standalone program with 42 metazoan genomes. I have tried to initiate the actual orthogroup inference phase but the program keeps getting stuck indefinitely on reading the all-vs. all results. I have double checked that each pair of ...
orthologs oma orthology written 8 months ago by eschang110 • updated 8 months ago by adrian.altenhoff620
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Comment: C: Correct formatting for IDs in OMA standalone .splice files to properly identify
... Realized I just responded to my own post: Okay great, this all in line with that I had gathered from the manual, but wanted to clarify before I started to put together those .splice files. Thanks so much! Cheers, Sally ...
written 8 months ago by eschang110
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Comment: A: Correct formatting for IDs in OMA standalone .splice files to properly identify
... Okay great, this all in line with that I had gathered from the manual, but wanted to clarify before I started to put together those .splice files. Thanks so much! Chers, Sally ...
written 8 months ago by eschang110
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Correct formatting for IDs in OMA standalone .splice files to properly identify splice variants
... I see that for the input .splice files, OMA standalone requires that the individual IDs are unique prefixes of your FASTA headers, and proteins that are splice variants of the same gene should be listed in the splice file like "ENSP00000384207; ENSP00000263741; ENSP00000353094". It looks like NCBI ...
orthologs oma orthology written 8 months ago by eschang110

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