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User: Carambakaracho

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Carambakaracho • 1.9k
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Bioinformatics specialist at a medical device company

Posts by Carambakaracho

<prev • 319 results • page 1 of 32 • next >
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Comment: C: Linking bacterial taxonomy to predicted genes with Prokka
... I never ran `Prokka` but does the "*FCHNPLMC*_00004" not relate back to any of your contigs? This is a bit bizarre. Anyhow, Prokka uses [Prodigal][1] for the prediction of CDS', you can run it alone - either in metagenome mode or, ideally on each bin of your assembly individually to allow it to trai ...
written 10 weeks ago by Carambakaracho • 1.9k
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Answer: A: gff3 header delimiter space or a tab
... This is a great question, and one why I 'love' the gff format so much. It is **not** explicitly defined. Period. See [definition of directives in gff3 format][1] - implicitly the documentation uses spaces, just as [ATpoint][2] illustrated, so I recommend spaces, too. Tabs are usually used for separa ...
written 11 weeks ago by Carambakaracho • 1.9k
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Answer: A: Where to find .ace format description
... I guess this is the best you can get: [Consed documentation/README.txt, chapter 26. ACE format definition][1] [1]: http://bozeman.mbt.washington.edu/consed/distributions/README.29.0.txt ...
written 11 weeks ago by Carambakaracho • 1.9k
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Comment: C: Joining vs merging paired ended reads
... depends a bit, but sure clustering merged and joined sequences from the identical organism would yield two OTUs. On the other hand, when the differences in one pair don't justify merging, how likely would it be the pairs ended up in two separate OTUs? ...
written 11 weeks ago by Carambakaracho • 1.9k
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Answer: A: Joining vs merging paired ended reads
... In addition to PANDAseq, you may want to look into [vsearch][1], [FLASH2][2] and [Pear][3], all of which can do overlap merging. A classic approach is to do the overlap merging where applicable and join/concatenate the pairs without sufficient overlap. The overlap is a function of the distribution o ...
written 11 weeks ago by Carambakaracho • 1.9k
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Comment: C: How do I decide between building a kmer-based or snp-based tree?
... Hi, this can't be answered with a simple "do it this way", even after you decided for one method you'll have tons of options. Take the simpler case of the kmers: you're tree may look fundamentally different based on the kmer length. Even worse for the SNP calling algorithms, you'l have many algorith ...
written 11 weeks ago by Carambakaracho • 1.9k
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Comment: C: Using Eggnog-mapper to categorize genes according to OG, without gene prediction
... the hmmer version gave me more results, as far as I recall. Diamond was way faster though ...
written 12 weeks ago by Carambakaracho • 1.9k
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Comment: C: Using Eggnog-mapper to categorize genes according to OG, without gene prediction
... I used the diamond database for a quick shot and then refined with more specific databases ...
written 12 weeks ago by Carambakaracho • 1.9k
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Answer: A: Using Eggnog-mapper to categorize genes according to OG, without gene prediction
... the [eggnog mapper][1] does no ab initio prediction, it annotates provided genes/proteins. You'll get additional annotation to the one prokka offers and can categorise based on that. [1]: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v1 ...
written 12 weeks ago by Carambakaracho • 1.9k
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Comment: C: Trim adapter of undefined length
... I stand corrected :-) ...
written 12 weeks ago by Carambakaracho • 1.9k

Latest awards to Carambakaracho

Scholar 5 days ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 7 weeks 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 weeks ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Commentator 3 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 4 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 4 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
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
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
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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
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
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
Scholar 11 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
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
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Teacher 16 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
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