User: Carambakaracho

gravatar for Carambakaracho
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Switzerland
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1 day ago
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2 years, 10 months ago
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k******@gmx.net

Bioinformatics and application specialist at a midsize bioinformatics company, Basel

Posts by Carambakaracho

<prev • 105 results • page 1 of 11 • next >
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Comment: C: PpWOX genes, Wuschel related homeobox genes, expressed in hypocotyl vasculature
... there's *[Pinus taeda][1]* [1]: https://www.ncbi.nlm.nih.gov/genome/11027 ...
written 1 day ago by Carambakaracho550
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Comment: C: Genome and transcriptome analyses in yeast
... Hi JJ, not much help, but looks pretty good to me. My only remark is - I don't understand why you would need known SNPs? For example, the [GATK germline pipeline][1] (and as such any germline snp calling) recommends to use as many samples as you can, but doesn't require SNPs, afaik. Cheers, C [ ...
written 1 day ago by Carambakaracho550
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Answer: A: GFF file multiple features for 1 gene region, how to collapse into 1?
... Filter for the gene features, either your gff column 3 or your bed file. However, a tRNA feature might rather be an exception than the rule. You can do this even with excel. ...
written 1 day ago by Carambakaracho550
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... let's put a bit more flesh to that bone http://www.ensembl.org/biomart/martview/ ...
written 3 days ago by Carambakaracho550
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
... In principle yes, provided you choose a clever reference. In case you plan to use more than one sequence, you need to make sure you know the corresponding coordinates - which you get from a msa of the original sequences (ok, there's ready aligned data out there, but you won't be able to use a msa as ...
written 8 days ago by Carambakaracho550
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Answer: A: Cell counting program needed
... Hi simon, my image analysis skills are a bit rusty, but maybe ImageJ can help you when you combine a - [Background substraction][1] (scroll down a bit to the section) to remove the uneven background - [Top-hat transform][2] to separate wells from cells - use one ofthe cell count techniques des ...
written 8 days ago by Carambakaracho550
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Comment: C: How To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
... maybe you should consider to open a separate question - you're question will be lost as a reply to this question. However, your problem (generate a MSA, a multi-sequence alignment) is fairly trivial in bioinformatics and there must be many threads around that topic. Programs that can do this are mus ...
written 8 days ago by Carambakaracho550
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Comment: C: An Alternative To Blastx With Speed Similar To Bowtie
... really? besides protein-protein searches, I understood this was one of the principal objectives of the algorithm. What do you mean? ...
written 10 days ago by Carambakaracho550
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Comment: C: MiSeq or HiSeq for metatranscriptome sequencing
... hi @toralmanvar though I agree in principle, in my experience, I had little improvement with longer Illumina read lengths in both WGS and WMS. For RNAseq, the paper you cited focuses on eukaryote transcriptome assembly. In prokaryotes, which make up most of what most people refer to as a microbiom ...
written 10 days ago by Carambakaracho550
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Comment: C: MiSeq or HiSeq for metatranscriptome sequencing
... > OP is interested in metatranscriptomic assembly which means he would like to > asses the functional activity of the microbial community Admitted, this wasn't phrased very clear. Anyway, OP also remained very silent for a few months ...
written 10 days ago by Carambakaracho550

Latest awards to Carambakaracho

Centurion 8 days ago, created 100 posts.
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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
Scholar 7 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 9 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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Scholar 3 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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Scholar 4 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: BAM/SAM to FASTA conversion
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion

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