User: dukecomeback

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dukecomeback30
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New User
Location:
China
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 1 month ago
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d***********@gmail.com

Posts by dukecomeback

<prev • 28 results • page 1 of 3 • next >
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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 4 months ago by dukecomeback30 • updated 4 months ago by Jean-Karim Heriche13k
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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 4 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 5 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 5 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 5 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 5 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 5 months ago by dukecomeback30 • updated 5 months ago by Rob2.2k
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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 5 months ago by dukecomeback30
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Comment: C: Eukaryotic Genome Annotation in 2016
... 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 6 months ago by dukecomeback30
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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 7 months ago by dukecomeback30

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