User: Carambakaracho

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Carambakaracho2.2k
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Bioinformatics specialist at a medical device company

Posts by Carambakaracho

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Comment: C: Good Books/Resources to learn metagenomic analysis?
... 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 10 weeks ago by Carambakaracho2.2k
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Comment: A: identifying the command for creating VCF file
... [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 4 months ago by Carambakaracho2.2k
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Comment: C: Howcomplete STAR annotation with NCBI Genebank
... 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 4 months ago by Carambakaracho2.2k
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Comment: C: Any good idea for bioinfo final presentation?
... 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 4 months ago by Carambakaracho2.2k
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Answer: A: Any good idea for bioinfo final presentation?
... 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 4 months ago by Carambakaracho2.2k
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Comment: C: Any good idea for bioinfo final presentation?
... 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 4 months ago by Carambakaracho2.2k
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Comment: C: What could make Bowtie2 miss legitimate hits?
... 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 4 months ago by Carambakaracho2.2k
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Comment: C: PCA with respect to observations and not to features in R
... [@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 4 months ago by Carambakaracho2.2k
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Comment: C: Bash script problem
... Just to make sure you're not hunting a ghost: the sorted bam in `s$1` contains all reads? I don't see any obvious show stopper, so maybe your input interferes with the call. You might want to try [parameter substitution][1] bedtools intersect -wa -a s${1} -b ${2} > KRAS_s${1} [1]: https ...
written 5 months ago by Carambakaracho2.2k
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Comment: C: Bash script problem
... Hi Steven, there's some additional info needed to support you: Is this the full body for the script? How do you run the bash script? Can you `echo $1` and `echo $2`? Does this yield what you expect? I don't think `>` should be the problem... ...
written 5 months ago by Carambakaracho2.2k

Latest awards to Carambakaracho

Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Popular Question 5 months ago, created a question with more than 1,000 views. For infer top level go category from GO:ID
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 9 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 9 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Appreciated 12 months ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 13 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 14 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 17 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
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Commentator 18 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 19 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 20 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format

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