User: dukecomeback
dukecomeback • 30
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- 1 week, 2 days ago
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Posts by dukecomeback
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... I think I've figure this out. It because that the sequences in the fasta file are output in one line. Some are too long for the exonerate.
Here is a perl script to re-type the fasta so each sequence would be output in multiple lines
#!/usr/bin/perl -w
use strict;
use Getopt::Long;
m ...
written 10 days ago by
dukecomeback • 30
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... I also run into this problem, don't know if you've figured it our? ...
written 10 days ago by
dukecomeback • 30
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... Hi, I want to cutoff the results by scores, but I hope there would be no length bias. ...
written 9 months ago by
dukecomeback • 30
• updated
9 months ago by
Jean-Karim Heriche ♦ 15k
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... Hi there,
When I run exonerate, I come across to this error: ** FATAL ERROR **: Unknown amino acid [U] exiting ...
Google lead me to this: https://github.com/nathanweeks/exonerate/issues/5, but the version I'm using (2.4.0) is supposed to be bug-fixed. So this link won't help me.
Do you have any ...
written 9 months ago by
dukecomeback • 30
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... I'm actually trying to build a genome annotation pipeline here. I hope to extract the overlap part from the two process to get some high quality genes.
...
written 10 months ago by
dukecomeback • 30
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... thanks for that link, WouterDeCoster, it can be accessed. :) ...
written 10 months ago by
dukecomeback • 30
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... Thank you so much for your sharing, I really didn't know the whole TopHat being deprecated thing. ...
written 10 months ago by
dukecomeback • 30
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... Thanks for your answer Damian.
I've built a whole pipeline base on your intelligence. I feed every software with repeat masked assembly sequences, so I didn't expected in the end I have to hint Augustus with RepeatMasker result again.
Anyway, so I guess the RepeatMasker hint file is adapted from th ...
written 10 months ago by
dukecomeback • 30
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... I combined 10 libraries before doing tophat+cufflinks and trinity+PASA assembling, end up with each process gave me hundred thousands of predicted transcripts. I believe there must be a lot of false positive. But would it be better if I run with each library respectively, then use some tools like cu ...
written 10 months ago by
dukecomeback • 30
• updated
10 months ago by
Rob ♦ 2.3k
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... Dear Mehmet,
I'm using AUGUSTUS 3.2.3, I also get this information: "Error: intron hint is too short" but no "error in add gene". I figure maybe I can just ignore it, do you think that's OK?
Sincerely,
Kang
...
written 10 months ago by
dukecomeback • 30
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