User: Carambakaracho
Carambakaracho • 2.3k
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Bioinformatics specialist at a medical device company
Posts by Carambakaracho
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... My apology, I'm a bit rusty using these commands, they're not in the focus of my job anymore. ...
written 10 weeks ago by
Carambakaracho • 2.3k
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... NCBI eutils: https://www.ncbi.nlm.nih.gov/books/NBK25500/
see also command line alternative edirect https://www.ncbi.nlm.nih.gov/books/NBK179288/ ...
written 10 weeks ago by
Carambakaracho • 2.3k
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... my last take on this was a workshop discussion 2/3 years ago, when the error rate made it very experimental and a bitchallenging. I guess that still holds true, but this is what it makes exciting, too ;-)
I would fill the gap of the unsupervised binning software with [metabat2][1], classification w ...
written 5 months ago by
Carambakaracho • 2.3k
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... [bcftools][1]? Though this is probably not what you need.
Similar to sam/bam format, sometimes the meta information contains the software used for variant calling (see the source tag, for example).
However, the tag is optional, not clearly specified and in most interpretations you get the softwar ...
written 6 months ago by
Carambakaracho • 2.3k
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... There's four assemblies at the NCBI:
https://www.ncbi.nlm.nih.gov/genome/browse/#!/eukaryotes/145/
In case your genes of interest are not annotated, but you know their sequence, why don't you blast them against your genome? ...
written 7 months ago by
Carambakaracho • 2.3k
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... bloody ****, I should pay attention to details...
Well, technically at least, DESeq2. EdgeR, and limma/voom are R . For what it's worth anyway ...
written 7 months ago by
Carambakaracho • 2.3k
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... I'm not the best source, as I'm behind on most of the active research, but I remember the feeling. For beginners it's not so easy to separate the wheat from the chaff, imo this would be your teacher's responsibility, though.
Let me give it shot: for data analysis milestones comparable with what yo ...
written 7 months ago by
Carambakaracho • 2.3k
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... I admit, had you asked me the questions above at the level of the OP with the breadth of bioinformatics today, I was overwhelmed, too and I started when [Koonin's COGs][1] where bleeding edge...
[1]: https://pubmed.ncbi.nlm.nih.gov/10592175/ ...
written 7 months ago by
Carambakaracho • 2.3k
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... One of a set of PCR duplicates? Can you filter them out with picard tools? What does the bam flag say? Did you try a different aligner, e.g. BWA mem? ...
written 7 months ago by
Carambakaracho • 2.3k
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... [@Santosh][1], thank you. This certainly among the best answers I've read on Biostars.
I'd like to add a tiny extension for transposition of tibbles [originally from stackoverflow][2], assuming genenames being the name of the first column:
dt <- d %>%
gather(var, val, 2:ncol(d)) ...
written 7 months ago by
Carambakaracho • 2.3k
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For infer top level go category from GO:ID
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For A: BAM/SAM to FASTA conversion
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