User: ciclistadan

gravatar for ciclistadan
ciclistadan30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 years, 8 months ago
Joined:
5 years, 8 months ago
Email:
c**********@gmail.com

Posts by ciclistadan

<prev • 6 results • page 1 of 1 • next >
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Does SPades contigs.fasta contain unassembled reads?
... Hopefully this is a simple question! I'm performing de novo assembly of viral metagenomic reads obtained from Ion Torrent sequencing with the intent of improving downstream alignment/BLAST characterization. SPades (v3.8.0) output creates contigs.fasta and scaffolds.fasta files. Do these files contai ...
de novo assembly assembly spades written 3.8 years ago by ciclistadan30
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esearch query does not return sorted results from NCBI EDirect
... I'm having trouble returning sorted results using the esearch tool from NCBI EDirect (v3.60). A quick search on their website shows good sorting by relevance for the search term "aurora" with top results "AURKA", "AURKB" from the gene database. When I use the eDirect esearch command line interface o ...
ncbi edirect esearch command-line entrez written 4.2 years ago by ciclistadan30 • updated 18 months ago by h.mon29k
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Comment: C: NGS preprocessing pipleine for ion torrent data
... What sort of targeted sequencing was performed? Whole exome, disease biomarker, cancer panel? Any of these methods is expected to produce large numbers of exact duplicates, so I wouldn't worry too much about that. You can also remove the "fix read mate" step since torrent sequencing won't be paired ...
written 4.2 years ago by ciclistadan30 • updated 3 months ago by RamRS26k
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Comment: C: nrow,ncol name used amino acid string
... maybe if you explain what you're trying to accomplish we can help a bit more? ...
written 4.8 years ago by ciclistadan30
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Answer: A: nrow,ncol name used amino acid string
... Not sure if I understand...or why you might be doing this sort of operation, but you can define the matrix dimensions (ncol and nrow) using the length of each list. If you're looking to name each row/column with the corresponding base, you can use dimnames. ``` seq1 = "GCATGCT" seq2 = "GATTACA" s1 ...
written 4.8 years ago by ciclistadan30 • updated 5 months ago by RamRS26k
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Comment: C: NCBI: how to obtain genomic context for arbitrary annotation release?
... I'm newer to sequence analysis, so thanks for pointing me to BioMart, seems like a great tool that's also easy to use. Poking around I found they also have a great timeline of genome assemblies to get an idea of the appropriate versions to select.  ...
written 4.9 years ago by ciclistadan30

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