User: Carambakaracho

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Carambakaracho2.2k
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Bioinformatics specialist at a medical device company

Posts by Carambakaracho

<prev • 364 results • page 1 of 37 • next >
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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 5 weeks 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 6 weeks 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 8 weeks 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 8 weeks 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 8 weeks 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 8 weeks 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 9 weeks 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 10 weeks 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 10 weeks ago by Carambakaracho2.2k
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Comment: C: Difference option in running BWA-MEM
... When you use `-Y` on secondary alignments the sequence that aligned to the primary alignment won't get hard clipped but softclipped, in my case I exploited that for split reads when a rearrangement occurred in the middle of the read. This means the clipped sequence will be preserved in the bam line ...
written 10 weeks ago by Carambakaracho2.2k

Latest awards to Carambakaracho

Popular Question 10 weeks ago, created a question with more than 1,000 views. For infer top level go category from GO:ID
Scholar 3 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 3 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 8 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 9 months ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Commentator 9 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 10 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 11 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
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
Scholar 14 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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
Guru 15 months ago, received more than 100 upvotes.
Commentator 15 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 15 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
Scholar 17 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 18 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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

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