User: dukecomeback
dukecomeback • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- China
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 2 years, 11 months ago
- Email:
- d***********@gmail.com
Posts by dukecomeback
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... Hi, I want to cutoff the results by scores, but I hope there would be no length bias. ...
written 9 weeks ago by
dukecomeback • 30
• updated
9 weeks ago by
Jean-Karim Heriche ♦ 12k
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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 10 weeks 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 3 months ago by
dukecomeback • 30
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... thanks for that link, WouterDeCoster, it can be accessed. :) ...
written 3 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 3 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 3 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 3 months ago by
dukecomeback • 30
• updated
3 months ago by
Rob ♦ 2.0k
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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 3 months ago by
dukecomeback • 30
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... Dear Damian,
In "8) Re-use PASA, Exonerate, SNAP, RepeatMasker as hints for Augustus and run gene predictions. The weighing of the hints is very subjective.", how can RepeatMasker output be hints for Augustus? Is there any chance that it's a typo?
Sincerely,
Kang ...
written 4 months ago by
dukecomeback • 30
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Comment:
C: Fast Qseq To Fastq Converter
... After installing scons, by simply type scons in the qseq2fastq directory, you can get the executbable qseq2fastq.
>qseq2fastq -i seq_fold/* you will get the results. ...
written 5 months ago by
dukecomeback • 30
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