User: dukecomeback

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dukecomeback30
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China
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1 month, 2 weeks ago
Joined:
3 years, 8 months ago
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Posts by dukecomeback

<prev • 30 results • page 1 of 3 • next >
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Answer: A: exonerate error while building index
... 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 9 weeks ago by dukecomeback30
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Comment: C: exonerate error while building index
... I also run into this problem, don't know if you've figured it our? ...
written 9 weeks ago by dukecomeback30
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Is the score from genewise and exonerate normalized by protein length?
... Hi, I want to cutoff the results by scores, but I hope there would be no length bias. ...
alignment written 11 months ago by dukecomeback30 • updated 11 months ago by Jean-Karim Heriche15k
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** FATAL ERROR **: Unknown amino acid [U] exiting ... in Exonerate
... 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 ...
software error genome alignment written 11 months ago by dukecomeback30
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Comment: C: combine or split, that's a question for transcriptome assembly
... 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 12 months ago by dukecomeback30
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Comment: C: combine or split, that's a question for transcriptome assembly
... thanks for that link, WouterDeCoster, it can be accessed. :) ...
written 12 months ago by dukecomeback30
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Comment: C: combine or split, that's a question for transcriptome assembly
... Thank you so much for your sharing, I really didn't know the whole TopHat being deprecated thing. ...
written 12 months ago by dukecomeback30
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Comment: C: Eukaryotic Genome Annotation in 2016
... 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 12 months ago by dukecomeback30
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combine or split, that's a question for transcriptome assembly
... 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 ...
assembly rna-seq written 12 months ago by dukecomeback30 • updated 12 months ago by Rob2.3k
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Comment: C: "Error: intron hint is too short" and "error in addgene "
... 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 12 months ago by dukecomeback30

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