User: Juke-34

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Juke-342.6k
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Posts by Juke-34

<prev • 364 results • page 1 of 37 • next >
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Comment: C: Why does bacterial codon table translate GTG start codon to V and not M?
... They do the same at EBI, they translate the alternative initiation codons as M. ...
written 12 hours ago by Juke-342.6k
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Comment: C: Extract every CDS sequences from a VCF file
... I'm not sure it is what you want but I have a perl script to extract CDS properly (concatenate them). Is is called `gff3_sp_extract_sequences.pl` and you can find in the [GAAS][1] repository. > gff3_sp_extract_sequences.pl --fasta genome.fa --gff annotation.gff -o cds.fa It extracts CDS per def ...
written 3 days ago by Juke-342.6k
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Answer: A: Is there a step-by-step tutorial on creating gene models for protists? (Maker?)
... It’s pity to drop funannotate after having spent so much energy. There is no way to fix your problem? Maker has also lot of dependencies... if you have installed it give it a try. There are plenty of documentation less verbose made by users on internet. If you are looking for other annoation tools ...
written 5 days ago by Juke-342.6k
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Comment: C: Generate GTF/GFF file (coordinates) from a FASTA annotated file.
... You would like to update an existing structural annotation based on this new data? Or you want an annotation based only on this trinity data? You can use PASA Indeed, GAWN or MAKER. What is your problem with PASA? You have to provide the trinity fasta file, the genome and a list of alignment tool t ...
written 5 days ago by Juke-342.6k
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Comment: C: Eukaryotic gene annotation on gene predictions
... Do you mean you look for a way to find gene functions? The common way to go is to run [Interproscan][1]. In one go you reach more than 20 different DB. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998142/ ...
written 7 days ago by Juke-342.6k
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Answer: A: How to extract fasta sequences from assembled transcripts generated by Stringtie
... I use `gff3_sp_extract_sequences.pl` from the [GAAS][1] repository. > gff3_sp_extract_sequences.pl --cdna --gff input.gtf --fasta genome.fa -o output.fa [1]: https://github.com/NBISweden/GAAS ...
written 9 days ago by Juke-342.6k
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Answer: A: How to add the start and stop position information to a gff file?
... I have a perl script for that purpose called `gff3_sp_add_start_and_stop.pl` > gff3_sp_add_start_and_stop.pl --gff infile.gff --fasta infile.fasta -o > output.gff You can specify the codon table to use (1 by default). It deals with start or stop codon that would be split over several exons. ...
written 10 days ago by Juke-342.6k
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Job: Bioinformatics scientist positions in Lund Sweden (last day application)
... 2 Bioinformatician positions Location: Lund, Sweden Type of employment: Permanent position Last application date 05.Sep.2019 https://lu.varbi.com/en/what:job/jobID:279454 ...
job bioinformatician written 14 days ago by Juke-342.6k
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Job: Bioinformatican with focus on Data Steward
... Bioinformatican – with focus on Data Steward Location: Uppsala, Sweden Type of employment: Permanent position Deadline 10 September. [https://www.uu.se/en/about-uu/join-us/details/?positionId=277048][1] [1]: https://www.uu.se/en/about-uu/join-us/details/?positionId=277048 ...
data steward job written 14 days ago by Juke-342.6k
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Comment: C: Annotation lifting to a different organism
... You should maybe consider another approach. Have a look here [enter link description here][1] table 5. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450745/ ...
written 14 days ago by Juke-342.6k

Latest awards to Juke-34

Appreciated 27 days ago, created a post with more than 5 votes. For A: Trinity strand specific: RF or FR
Popular Question 29 days ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Prophet 6 weeks ago, created a post with more than 20 followers. For Orientation of PE reads a review of --fr --ff and --rf meanings
Student 7 weeks ago, asked a question with at least 3 up-votes. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 5 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 5 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 5 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Appreciated 6 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
Scholar 7 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 8 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 9 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Appreciated 11 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Appreciated 11 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 11 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Appreciated 11 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Popular Question 12 months ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar 14 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Popular Question 16 months ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden

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