User: Juke-34

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Juke-341.2k
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Posts by Juke-34

<prev • 223 results • page 1 of 23 • next >
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Comment: C: extracting the longest transcript in a fasta file
... Have a look [here][1] it has been already discussed [1]: https://www.biostars.org/p/290651/ ...
written 8 days ago by Juke-341.2k
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Answer: A: How to properly modify genome .gff and .fa to combine 2 loci that are really 1 g
... You could use [this service][1] to look at the longest ORF in each exon. For the first cds piece it's easy it is 0 (If you have your complete gene) A good way would be to load your two genes in a genome browser allowing manual curation, and you merge your genes manually, then you download the resu ...
written 14 days ago by Juke-341.2k
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Comment: C: Genes, Isoforms, Proteins?
... I think you can find nice definitions on google, isn't it ? Is there something particular that you are wondering ? Have a look [here][1] it is a really nice documentation. I think you could find lot of things about isoforms (Alternative transcripts). [1]: ftp://ftp.sanger.ac.uk/pub/project/havan ...
written 15 days ago by Juke-341.2k
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Comment: C: How to generate GFF3 format that I want?
... I implemented a parser to check, fix, pad any kind of gtf and gff to create complete and standardize gff3 format. If you are interested you will find it in the github [NBISweden][1] repository. Follow the installation instruction [here][2], then the easiest is to use this script gxf_to_gff3.pl If y ...
written 24 days ago by Juke-341.2k
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Comment: C: How to generate GFF3 format that I want?
... Why are you talking about gff3 ? Gff3 is a format with 9 columns. Here is a 5 columns tabulated format. It is definitely not gff3 format. ...
written 27 days ago by Juke-341.2k
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Comment: C: splice junction information with hisat2
... I don’t know the use of those options but for sure it is fine without to determine the spicing sites. For the extraction of spicing sites I have used fasta_domainExtractor_JD.pl from the [NBIS/GAAS][1] repository but it is not really adapted for what you want. You can get inspiration from this scr ...
written 4 weeks ago by Juke-341.2k
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Comment: C: splice junction information with hisat2
... You’re welcome. The problem is you provided a path but no file name. Instead of “/data/memona/hisat2-2.1.0/result/” do “/data/memona/hisat2-2.1.0/result/splice_sites.tsv” and it should be fine. ...
written 4 weeks ago by Juke-341.2k
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Answer: A: splice junction information with hisat2
... Hi blooming.daisy333, It is explained in the [manual][1]. You have to use the option --novel-splicesite-outfile. Be careful there is an error how left splice sites are reported as I mentioned [here][2]. [1]: https://ccb.jhu.edu/software/hisat2/manual.shtml [2]: https://github.com/infphilo/his ...
written 6 weeks ago by Juke-341.2k
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Comment: C: Uploading data files to Webin upload area under Linux
... Interesting... I have tried from two different location in Sweden without success.... both are in universities.... maybe a new firewall protection ... Ok, I have tried using a vpn and now it is working !! ...
written 11 weeks ago by Juke-341.2k
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Comment: C: Uploading data files to Webin upload area under Linux
... It is the third day I try without success... ftp 193.62.192.11 and ftp webin.ebi.ac.uk the same... 421 Service not available, remote server has closed connection :( ...
written 11 weeks ago by Juke-341.2k

Latest awards to Juke-34

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Trinity strand specific: RF or FR
Appreciated 4 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 7 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
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Appreciated 15 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 15 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question 16 months ago, created a question with more than 1,000 views. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
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Scholar 24 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 2.5 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 3.1 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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