User: dukecomeback

gravatar for dukecomeback
dukecomeback40
Reputation:
40
Status:
New User
Location:
China
Last seen:
6 months, 2 weeks ago
Joined:
5 years, 8 months ago
Email:
d***********@gmail.com

Posts by dukecomeback

<prev • 36 results • page 1 of 4 • next >
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Comment: A: How to extract fasta sequences from assembled transcripts generated by Stringtie
... use gffread, you can find it in cufflink package ...
written 8 months ago by dukecomeback40
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Answer: A: Automagically Remove "Badly" Aligning Sequence From Multiple-Sequence Alignment
... https://github.com/dukecomeback/bad-sequence-remover ...
written 14 months ago by dukecomeback40
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Comment: C: GMAP error - Problem Sequence: TRINITY_DN422143_c0_g1_i1 (301 bp)
... I'm not so sure if it has something to do with the header of the fasta sequences. Keeping the header of sequences in simple characters maybe help. ...
written 15 months ago by dukecomeback40
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Answer: A: augustus output - how is the incompatible hint groups determined?
... I'm a little disappointed with Augustus, some times I know the hint is corrected, however no matter how hard I try, Augustus just do not obey the hint. Feel won't love anymore. ...
written 15 months ago by dukecomeback40
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Comment: C: Amino Acid matrices freely downloadable url
... Hi, I'm quiet new to evolution, do you know why there is so many version of Jones matrices there? Thank you very much. ...
written 16 months ago by dukecomeback40
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Comment: C: GMAP error - Problem Sequence: TRINITY_DN422143_c0_g1_i1 (301 bp)
... Dear TrentGenomics, have you solved this? I'm also stucked here ...
written 22 months ago by dukecomeback40
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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 2.1 years ago by dukecomeback40
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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 2.1 years ago by dukecomeback40
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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 2.9 years ago by dukecomeback40 • updated 2.9 years ago by Jean-Karim Heriche22k
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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 2.9 years ago by dukecomeback40

Latest awards to dukecomeback

Popular Question 15 months ago, created a question with more than 1,000 views. For look for the old version blast (not blast+)
Popular Question 22 months ago, created a question with more than 1,000 views. For what is pairwise dN/dS used for?

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