User: mtollis

gravatar for mtollis
mtollis30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 years, 4 months ago
Joined:
6 years, 4 months ago
Email:
m******@asu.edu

Posts by mtollis

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Available software for checking all species have a 4d site for a particular codo
... If your focal species is a reference species in your alignment as in one constructed with MULTIZ, and it has available CDS annotations, you should try msa_view from the PHAST package. http://compgen.cshl.edu/phast/ ...
written 3.4 years ago by mtollis30
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Comment: C: how to find out repeats ancestral to primates and use them as neutral model?
... upvoted this because it needs to be highlighted as the best answer. ...
written 5.0 years ago by mtollis30
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Comment: C: Augustus Training Time
... As this is a separate question, it should have been posted as a new thread. The only way to speed things up is to configure maker using MPI. It takes me about 6 days on 16 processors to finish one round on a ~150,000 scaffold ~2Gigabase vertebrate genome with protein evidence. ...
written 5.6 years ago by mtollis30
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Answer: A: kmergenie generates histo files but no histograms!
... Was this ever resolved? I have the same issue, thanks. ...
written 5.7 years ago by mtollis30
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Answer: A: Missing or disappearing output RepeatMasker
... From the RepeatMasker developer, who suggested the following two fixes: "The culprit is the processing of the alignment data using the "-a" flag. I tracked it down to a bug in a routine which handles joining DNA transposons. The ugly match set was: 334 C21533332 2812 2859 + HAT1_DR#DNA/hAT-Ac 598 ...
written 5.7 years ago by mtollis30
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Comment: A: Missing or disappearing output RepeatMasker
... Also, the data is a vertebrate-sized genome with hundreds of thousands of scaffolds. However, I have had RM work on these kinds of datasets with no problems before. ...
written 6.1 years ago by mtollis30
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Comment: A: Missing or disappearing output RepeatMasker
... Here is the command I used: RepeatMasker -no_is -pa 16 -species "vertebrates" -a -html -gff genome.fasta And this is an error message I found in the standard output. Can't call method "getScore" on unblessed reference at /home/mtollis/RepeatMasker/PRSearchResult.pm line 164. ...
written 6.1 years ago by mtollis30
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Missing or disappearing output RepeatMasker
... I have received this message recently while using makeblastdb for rmblast in RepeatMasker, and it is a real head-scratcher for me.  After no errors and completely running through all cycles, RepeatMasker finishes but there are no output files. The only trace of the analysis is the rmblastdb.log fil ...
makeblastdb repeatmasker written 6.4 years ago by mtollis30 • updated 18 months ago by gbdias90

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Popular Question 5.0 years ago, created a question with more than 1,000 views. For Missing or disappearing output RepeatMasker

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