User: Carambakaracho

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Carambakaracho1.8k
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Switzerland/Basel
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Bioinformatics and application specialist at a midsize bioinformatics company, Basel

Posts by Carambakaracho

<prev • 306 results • page 1 of 31 • next >
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Comment: C: How to calculate the density of alternative alleles as a ratio in a window of 10
... Th image you reference does not feature alternative alleles, to me it looks like it's displaying SNP density (as some sort of SNP/Non-SNP ratio?). For allele frequencies, you would rather expect discrete step like sections, depending on ploidy (for example three states `[0] - [0.5] - [1]` for hetero ...
written 16 hours ago by Carambakaracho1.8k
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Comment: C: Database Recommendations for 16S-seq of the V4 Region
... I might be missing the essential information on my mobile phone screen, but I to me the [Genome Taxonomy Database][1] seems much genome centric. It looks like a great resource, but what makes you believe it would be a well suited source for a 16S phylogeny? Silva is in my opinion the gold standard ...
written 3 days ago by Carambakaracho1.8k
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Comment: C: Bioinformatician, a jack of all trades, but in the eye of the CV-beholder a mast
... I do believe the accomplishments section is the most important part in the CV, too. This is the section where I read whether an applicant solved problems comparable to the ones he would face in the advertised position ...
written 3 days ago by Carambakaracho1.8k
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Comment: C: Beginner pipeline to compare SSU in sample to tree of SSUs
... Sure. To be fair, I got way less lucky than [Mensur][1] when attempting to use 16S sequences from pretty much any illumina short read bacteriel assembly. My assemblies broke frequently exactly at the 16S locus, while 5S and 23S made it in one or the other contigs. I used SortMeRNA and attempted s ...
written 7 days ago by Carambakaracho1.8k
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Comment: C: Beginner pipeline to compare SSU in sample to tree of SSUs
... RNAmmer and Barrnap are used to predict ribosomal genes in full genomes - is this WGS data? Do you plan to assemble these reads? ...
written 8 days ago by Carambakaracho1.8k
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Comment: C: STAR aligner maps 0 reads to multiple loci, but 3.7% to too many loci - meaning?
... a non exhaustive, short comment: STAR dismisses reads mapped to "*too many loci*" while it keeps "*mutlimappers*". There's a parameter to control the "*too many loci*" threshold, I just don't know it by heart... ...
written 10 days ago by Carambakaracho1.8k
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Comment: C: What's the best practice to do scaffolding?
... > Do I need to do scaffolding on this assembly? nope. There's always a slight chance you might be able to merge one or the other scaffold but it's unlikely. You can try to polish the assembly, though. ...
written 13 days ago by Carambakaracho1.8k
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Comment: C: Query coverage in global alignment
... uhoh, my bad... To recompense for my poorly qualified comment let me direct you to [the help page][1] of `needleall`. I believe their layout was bad already when the internet was born, and it's only topped by the obscure commandline switches. My best guess is the `-awidth3` switch does what you wan ...
written 14 days ago by Carambakaracho1.8k
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Comment: C: Reverse Complement Reads in BAM File
... while keeping the alignement coordinates? Or just reverse complementing the sequence? ...
written 14 days ago by Carambakaracho1.8k
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Comment: C: Query coverage in global alignment
... Dear el97004, you compare two protein sequences using an [alignment algorithm][1]. There's a few misconceptions in you're question 1. Coverage usually describes sequencing depth of DNA sequencing 2. Sequence alignments yield similarity scores (like you get), not coverage [1]: https://en.wikipe ...
written 14 days ago by Carambakaracho1.8k

Latest awards to Carambakaracho

Scholar 4 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 7 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 5 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 5 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 6 months ago, received more than 100 upvotes.
Commentator 6 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 6 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 7 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 8 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 8 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
Scholar 10 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 10 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
Scholar 13 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 14 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 15 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 16 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori

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