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User: Carambakaracho

gravatar for Carambakaracho
Reputation:
620
Status:
Trusted
Location:
Switzerland
Last seen:
an hour ago
Joined:
3 years ago
Email:
k******@gmx.net

Bioinformatics and application specialist at a midsize bioinformatics company, Basel

Posts by Carambakaracho

<prev • 127 results • page 1 of 13 • next >
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Comment: C: How to link the assembly accession with the chromosome accession for prokaryotic
... The README says it's manually updated. I tend to believe you'll see a more complete picture when using the `prokaryotes.txt` (computationally updated...) ...
written 11 days ago by Carambakaracho • 620
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Comment: C: Mock Metagenome Gene Content
... no real answer, but a different dataset http://mockrobiota.caporasolab.us/ ...
written 13 days ago by Carambakaracho • 620
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Answer: A: Filtering noise out of SAM file using CIGAR
... as Wouter points out above, [by specification][1] hard clipping is the first or last operation. Soft clipping is the first or last operation, unless hard clipping occurs. And as Devon wrote, you can influence clipping behavior in most aligners. to filter out reads you can use something like this (u ...
written 13 days ago by Carambakaracho • 620
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Comment: C: How to link the assembly accession with the chromosome accession for prokaryotic
... As vkkodali wrote, use the `prokayotes.txt`. However, there's no need to join, one can filter on the `Reference` column. The NCBI discriminates between manually selected *reference* (exist for common lab organisms) and computationally selected *representative* genomes (exists for each species, almos ...
written 14 days ago by Carambakaracho • 620
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Comment: C: SILVA taxonomy ranks
... cool, thanks, too ...
written 14 days ago by Carambakaracho • 620
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Answer: A: SILVA taxonomy ranks
... It's not clear from the [README][1], but you're supposed to use the mapping file `tax_slv_[ls]su_VERSION.txt`, for example [tax_slv_ssu_132.txt][2] to resolve the rank of each class. There used to be some Megan compatible files, but I don't find them (or it's the qiime files). These had a fixed nu ...
written 14 days ago by Carambakaracho • 620
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... this can have many reasons, the most frequent problem is a typo. In case you want more profound help, please post your exact command here. Please use the `101010` code formatting button (fifth in the ribbon above) ...
written 14 days ago by Carambakaracho • 620
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Comment: C: Overall alignment 0.00%
... What genome do you align against? Where does your data come from? What was your command? Does your reference genome match your data? What is your question? So I got stuck here. ...
written 18 days ago by Carambakaracho • 620
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Answer: A: How much data and how many libraries do we need for de-novo assembly?
... 1. For bacteria I recommend one PacBio SMRT cell (should be sufficient for roughly >30x) or >30x Nanopore in combination with >20x standard Illumina PE. This often lead to very good assemblies out of the box using the right assemblers or long read assembly/polishing combinations. However, 5 ...
written 21 days ago by Carambakaracho • 620
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Comment: C: Synonym for LOC
... >I just came to the conclusion that there was no information for them? That's sort of the easy way, but as jrj,healey wrote above you can always blast them and draw conclusions based on the results. ...
written 23 days ago by Carambakaracho • 620

Latest awards to Carambakaracho

Scholar 14 days ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Centurion 8 weeks ago, created 100 posts.
Voter 9 weeks ago, voted more than 100 times.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
Scholar 3 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 3 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 5 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 5 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Autobiographer 6 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Supporter 7 months ago, voted at least 25 times.
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: BAM/SAM to FASTA conversion
Appreciated 8 months ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: BAM/SAM to FASTA conversion
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