User: Juke-34

gravatar for Juke-34
Juke-341.1k
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Sweden
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Joined:
3 years, 6 months ago
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Posts by Juke-34

<prev • 205 results • page 1 of 21 • next >
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Comment: C: Finding the parent gene of pseudogene in mouse
... I would definitely prefer to use ML tree if I had the possibility. And between NJ tree and rigorous Blast, I will turn without hesitation to the NJ tree. ...
written 8 days ago by Juke-341.1k
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Comment: C: Denovo genome assembly annotation
... .................... ...
written 5 weeks ago by Juke-341.1k
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Comment: C: Denovo genome assembly annotation
... I don t have any tutorial. It should be pretty straightforward to use. Have you tried to launch it at least ? Have you read the readme or/and the help ? If you run into problems we will be happy to help you. ...
written 5 weeks ago by Juke-341.1k
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Answer: A: Denovo genome assembly annotation
... Here are described the best approaches: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207268/][1] Using Genemark alone probably will give you a first good draft of your annotation. In most of case it would be enough. It depends what you plan to do next. Genemark with proteins (Gnemark-P) or ESTs ...
written 5 weeks ago by Juke-341.1k
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Comment: C: Guessing The Quality Scale In Fastq Files
... Thanks, Updated now ...
written 5 weeks ago by Juke-341.1k
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Comment: C: Frame of CDS on reverse strand: I don't get it or is there a problem in file?
... It looks to be an error in the PlasmoDB gff file. It occurs more often than people think... Even in serious DBs. ...
written 6 weeks ago by Juke-341.1k
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Answer: A: Transdecoder - log likelihood for which purpose ?
... I found my answer in the supplement of the trinity paper [here][1] [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/bin/NIHMS537313-supplement-supplementary_text.pdf ...
written 8 weeks ago by Juke-341.1k
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Comment: C: Reference annotation file contains only transcript and CDS information, how to a
... You could read line by line the file and duplicate all CDS feature and modify the 3th column to "exon". This newly created gff annotation will then work into the pipelines. ...
written 8 weeks ago by Juke-341.1k
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Transdecoder - log likelihood for which purpose ?
... I don't get the use of log-likelihood score by Transdecoder. I googled and didn't find satisfying information. Someone could provide some hints ? Why using likelihood when searching longest ORF ? I have the feeling it assumes that some frames are more likely than some others... but why ? In a tran ...
gene sequence written 8 weeks ago by Juke-341.1k
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Comment: C: Maker failure on almost all contig
... BTW be careful using stringtie gff3 output, maker doesn't complain but it is not use if it is given as an gff alignment (est_gff or altest_gff). ...
written 11 weeks ago by Juke-341.1k

Latest awards to Juke-34

Supporter 5 weeks ago, voted at least 25 times.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 12 weeks ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
Guru 4 months ago, received more than 100 upvotes.
Appreciated 10 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question 11 months ago, created a question with more than 1,000 views. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Centurion 19 months ago, created 100 posts.
Scholar 19 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 2.1 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names

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