User: Carambakaracho
Carambakaracho • 550
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Bioinformatics and application specialist at a midsize bioinformatics company, Basel
Posts by Carambakaracho
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... there's *[Pinus taeda][1]*
[1]: https://www.ncbi.nlm.nih.gov/genome/11027 ...
written 1 day ago by
Carambakaracho • 550
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... 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
Carambakaracho • 550
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... 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
Carambakaracho • 550
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... let's put a bit more flesh to that bone
http://www.ensembl.org/biomart/martview/ ...
written 3 days ago by
Carambakaracho • 550
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... 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
Carambakaracho • 550
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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
Carambakaracho • 550
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... 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
Carambakaracho • 550
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... 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
Carambakaracho • 550
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... 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
Carambakaracho • 550
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... > 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
Carambakaracho • 550
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For A: BAM/SAM to FASTA conversion
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For A: BAM/SAM to FASTA conversion
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