User: Carambakaracho

gravatar for Carambakaracho
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Switzerland
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2 years, 6 months ago
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k******@gmx.net

Bioinformatics and application specialist at a midsize bioinformatics company, Basel

Posts by Carambakaracho

<prev • 48 results • page 1 of 5 • next >
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Answer: A: How is the job outlook in 2020 ?
... here's some (though 2015) estimates on available data in 2025: [Stephens et al. estimated the available genome data to match the amount of video material on Youtube bey 2025][1], Erika Check Hayden [summarized this on Nature News][2] at that time. Based on this, and my observation that sequencing ...
written 2 days ago by Carambakaracho270
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Comment: C: Tool to do Variant calling from contigs data
... My apology, this is no answer, but I'm curious and would love to know available solutions as well. The best a quick search yielded is Heng Li's [fermikit][1]. Maybe you can skip the assembly stage and feed it the assemblies? [1]: https://github.com/lh3/fermikit ...
written 5 days ago by Carambakaracho270
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Comment: C: Genomic statistics from gtf
... My apology for disrupting the flow, this was supposed to become a comment based on Alex' earlier comment rather than a separate answer. ...
written 9 days ago by Carambakaracho270
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Comment: A: Genomic statistics from gtf
... You might also check out [the gff3 format][1], which is an important extension to the gff2/gtf format. For both formats there are parsers in many languages, [BioPerl][2] for example, of course [Python has an extensions][3] as well, for example [gffutils][4] [1]: http://gmod.org/wiki/GFF3 [2]: ...
written 9 days ago by Carambakaracho270
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Comment: C: are all gff file provided by NCBI clearly annotated with gene and protein sequen
... For anything but bacteria I recommend to look at [ensembl genomes][1] as well, for example the pig genome there: [Sus scrofa][2] When you know there were groups with better annotation, the ensembl is more likely to integrate such annotation for many genomes, with exception of JGI genomes in my expe ...
written 10 days ago by Carambakaracho270
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Answer: A: are all gff file provided by NCBI clearly annotated with gene and protein sequen
... Welcome to the world of NCBI genomes. There is no definite quality standard as far as I know, however, there is the "RefSeq category" (see [NCBI assembly help][1] page, somewhere halfway trough) You might be luckiest with *reference* or *representative* genomes, but there's no guarantee on the annot ...
written 10 days ago by Carambakaracho270
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Comment: C: Differences between trimming tools: cutadapt, bbduk and sickle
... > phred algorithm [...] leaves the longest area with average quality above the limit you specify such that it cannot be extended without adding an area of average quality below the limit you specify dear Brian, thanks for your outstanding program. Please allow me to note, that the description of ...
written 12 days ago by Carambakaracho270
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Comment: C: GTF file for Bombyx Mori
... you might be able to transfer the gene_id from CDS to exons (or convert the parent attribute to gene_id). This is one of the ugly conversion limitations. Btw, the problem with GFF files is almost always the 9th column - this is where the specs get really "flexible" ...
written 16 days ago by Carambakaracho270
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Comment: C: GTF file for Bombyx Mori
... thanks, I didn't know they still maintain a gtf section... ...
written 16 days ago by Carambakaracho270
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Answer: A: GTF file for Bombyx Mori
... Hi Sandeep, the file you have is [gff3 format][1] and htscount seems to expect [gff2 format][2] (gtf is pretty much gff2). I'm surprised it wouldn't work with gff3, either it requires some annotation field or fails on the header? Anyway, you might try [gffread][3] to convert between the formats, ...
written 16 days ago by Carambakaracho270

Latest awards to Carambakaracho

Autobiographer 12 days ago, has more than 80 characters in the information field of the user's profile.
Scholar 16 days ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Supporter 9 weeks ago, voted at least 25 times.
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: BAM/SAM to FASTA conversion
Appreciated 3 months ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion

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