User: Carambakaracho

gravatar for Carambakaracho
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750
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Switzerland
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7 hours ago
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3 years, 2 months ago
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k******@gmx.net

Bioinformatics and application specialist at a midsize bioinformatics company, Basel

Posts by Carambakaracho

<prev • 146 results • page 1 of 15 • next >
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Comment: C: Changing FASTQ format from sense to antisense
... Dear miyagi, welcome on Biostars. I admit, I fail on this formating, too. Please use the code button `101010` on the fastq part to make it better readable. And please add the error from slam dunk, in case people recognize the error. ...
written 18 hours ago by Carambakaracho750
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Comment: C: Why does bacterial codon table translate GTG start codon to V and not M?
... > In fact, such is biology’s disregard for what few rules we attempt to hold dear, that translation can actually occur from pretty much any initial codon. The degree of translation simply changes. Thanks for sharing this one. I sort of fundamentally believed in the canonical start codons with ex ...
written 3 days ago by Carambakaracho750
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Comment: C: Number of genomes sequences in NCBI
... I have yet another one: 294 This is based on [eukaryotes.txt][1] in [genome_reports][2] instead of the [assembly_reports][3] (filtered on SubGroup for mammals and counting unique organism names) Most likely the rates are at which the files are refreshed are different. [1]: ftp://ftp.ncbi.nih.go ...
written 6 days ago by Carambakaracho750
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Comment: C: What does <*> mean in a vcf file?
... the `<*>` is nowhere mentioned explicitly, but here's some more hints towards wildtype GATK: [What is a GVCF and how is it different from a 'regular' VCF?][1] SciLifeLab (AM Barrio): [What is gVCF][2] [1]: https://software.broadinstitute.org/gatk/documentation/article.php?id=4017 [2] ...
written 6 days ago by Carambakaracho750 • updated 6 days ago by RamRS20k
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Comment: C: What does <*> mean in a vcf file?
... [Illumina gVCF spec][1] is equally vague, at least I guess it's a non specified alternative allele: > - REF: Reference bases: A,C,G,T,N; there can be multiple bases. The value in the POS field refers to the position of the first base in the string. For simple insertions and deletions in which ei ...
written 6 days ago by Carambakaracho750
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Answer: A: Gff3 - moving an annotation from scaffold level to pseudomolecule level
... Hi Philipp, might [liftOver][1] do what you want? Though my impression is that data prep might just take as long as writing the script. [1]: https://genome.sph.umich.edu/wiki/LiftOver#Lift_genome_positions ...
written 10 days ago by Carambakaracho750
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Answer: A: FLASh parameters for 250 read length
... The answer depends on your library prep: 1000 bp fragments -> max 50 bps overlap should do the trick. 400 bp fragments -> more in the range of 200 bps max overlap, maybe even more. I never used the min overlap. Anyway I'd strongly recommend to iterate over different options. ...
written 11 days ago by Carambakaracho750
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Comment: C: how remove stopcodons from a GFF
... hi there, welcome to Biostars. Unfortunately, your question seems a bit incomplete. The comment (that ideally should be code formatting see `101010` button) indicates you use blat. What do you want to achieve? what is your command that fails? GFF is a wide field and I'm unsure whether this is the ac ...
written 11 days ago by Carambakaracho750
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Comment: C: Avoid download limit from NCBI entrez with Biopython using API key
... Hi Shred, great. BTW, beyond narcissism, you'll help figure people in the future if an answer was helpful by upvote/accept. Especially on such niche topics like the e-utils ;-) ...
written 12 days ago by Carambakaracho750
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Comment: C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
... There's 20 amino acids, it's fairly easy to create that list from the chemical formula in wikipedia, read it in a dictionary/hash, loop over your sequences, add up Cs and Ns, compute the ratio. Doesn't seem very complicated, or do I miss something ...
written 12 days ago by Carambakaracho750

Latest awards to Carambakaracho

Scholar 12 days ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 9 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 12 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Centurion 4 months ago, created 100 posts.
Voter 4 months ago, voted more than 100 times.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
Scholar 5 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 7 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 7 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 8 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Supporter 10 months ago, voted at least 25 times.
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: BAM/SAM to FASTA conversion
Appreciated 11 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: BAM/SAM to FASTA conversion

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