User: Carambakaracho

gravatar for Carambakaracho
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440
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Location:
Switzerland
Last seen:
3 hours ago
Joined:
2 years, 8 months ago
Email:
k******@gmx.net

Bioinformatics and application specialist at a midsize bioinformatics company, Basel

Posts by Carambakaracho

<prev • 76 results • page 1 of 8 • next >
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Comment: C: A way to verify that GFF and Fasta files make a valid pair (came from the same p
... One additional note: You'll make your and your colleagues life easier in the future if you include the sequence part in the gff directly. Any gff can contain an arbitrary sized sequence section after a `##FASTA` directive See other syntax section in the [gff specification][1] [1]: https://github ...
written 1 day ago by Carambakaracho440
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Comment: C: Can I make GFF3 from either GFF or genome fasta file?
... while I certainly like the perl one liner solution, there's a few problems with the gff3 like format. Col3 is better represented as something like a CDS, mRNA or similar higher order class and `$F[4]` better goes to the end and there must not be a period following the coordinate perl -nae 'prin ...
written 3 days ago by Carambakaracho440
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Comment: A: Construction of download links for genbank files from NCBI gene database
... This is an internal ID, as far as I know (might be the old outphased GI number), see https://www.ncbi.nlm.nih.gov/nuccore/568815581 Maybe a batch search can help you https://www.ncbi.nlm.nih.gov/sites/batchentrez There are more ways to have this automated, but none of those are trivial. Do you r ...
written 3 days ago by Carambakaracho440
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Comment: C: Creating your own substitution matrix from an alignment
... Hi mdsiddra, does this code really fail in the last block? This is close to impossible to reproduce without your exact input file `seq_file2.aln`. But you certainly are able to figure out the problem on your own. My first guess from the error message is that your input data contains illegal characte ...
written 3 days ago by Carambakaracho440
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Comment: C: Assembly of wheat genome
... You might want to look into the latest [Quast 5.0][1] which includes their new LG (large genome) module that you can combine with alignment against the public reference. @h.mon the St. Petersburg folks behind Spades and Quast etc. seem to have moved to a new website [http://cab.spbu.ru/][2] [1] ...
written 4 days ago by Carambakaracho440
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Comment: C: GC content in metagenomic data
... What sort of metagenomic samples are you extracting from tissue? Metagenomic samples are a more or less complex and diverse collection of organisms, some of which might be low GC. ...
written 4 days ago by Carambakaracho440
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Comment: C: Diamond vs GhostX vs RapSearch2?
... what a great tiny test, I'd valued this 5 thumbs if I could ...
written 6 days ago by Carambakaracho440
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Comment: C: Metagenomic classification by custom database
... Hi Mikael, fyi, general good practice is to mark helpful answers with thumbs up and in case it was the correct answer with accepted answer, so others can spot the best solutions faster ...
written 6 days ago by Carambakaracho440
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Comment: C: BWA gives wrong number of input sequences
... Hi Agata, these are most likely sequences mapping to more than one location. The BAM doesn't tell you the number of input sequences but the number of alignments against the reference ...
written 7 days ago by Carambakaracho440
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Answer: A: Metagenomic classification by custom database
... To me it sounds all you need is some super fast blast like functionality. In case I didn't misinterpret your request try either [Benjamin Buchfink's diamond][1] (against protein database) or [NCBI magicblast][2] (against DNA database). The abundance table then is a simple script using hash/dictiona ...
written 7 days ago by Carambakaracho440

Latest awards to Carambakaracho

Scholar 6 days ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 7 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 7 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Autobiographer 9 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 10 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Supporter 4 months ago, voted at least 25 times.
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: BAM/SAM to FASTA conversion
Appreciated 5 months ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion

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