User: ctseto

gravatar for ctseto
ctseto70
Reputation:
70
Status:
Trusted
Location:
Last seen:
1 month, 2 weeks ago
Joined:
5 years, 8 months ago
Email:
c*****@gmail.com

about me

Posts by ctseto

<prev • 15 results • page 1 of 2 • next >
0
votes
1
answer
119
views
1
answer
FASTA contaminant contig mapping/pulldown?
... Curious to see how much got through my pulldown of contaminant fastq in NGS by assessing what comes out in the de novo assembly. Would using something like minimap to map reads against reference be appropriate? I imagine there are better methods than to make sam/bams... ...
fasta assembly written 6 weeks ago by ctseto70 • updated 6 weeks ago by Charles Warden7.0k
0
votes
1
answer
143
views
1
answers
Comment: C: How can I analyse NGS data of microbiome (For beginner)?
... qiime2.org has a decent tutorial for the OTU table generation and the like. As you're starting out, may want to pick up toy data and run with it first; as tempting as it is to throw your real data into the mix, the more confident/familiar/competent you are with your data, the less "oops, gotta chang ...
written 7 weeks ago by ctseto70
1
vote
1
answer
124
views
1
answers
Answer: A: Identify AMR genes from WGS bacterial sequence
... "Compare the sequence of B. mayonii to other bacterial sequences that are deposited in NCBI" De novo assembly (SPAdes or Megahit with appropriate read QCing), followed by similar annotation techniques as those in the B. mayonii paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5193363/pdf/pone.016 ...
written 8 weeks ago by ctseto70 • updated 8 weeks ago by genomax69k
0
votes
1
answer
167
views
1
answers
Answer: A: kraken2 different bacteria read counts on custom database
... If you like reading kraken --output files, for each contig You might have Bacteria:1 9606:12 0:1000 (where 0 is unclassified) Eliminate the host 9606 and it turns to Bacteria:1 0:1012, the vote switches to Bacteria Eliminate the host 9606 and it turns to Bacteria:N 0:1000+(12-N), the vote switches t ...
written 8 weeks ago by ctseto70
2
votes
0
answers
174
views
0
answers
Best SAM flags to evaluate host contamination
... After generating a BAM, looking at which reads map to a known contaminant (human host) and which don't (theoretically, gut contents across tree of life). From BAM, was thinking of extracting paired end reads using `samtools fastq -1 R1.fastq -2 R2.fastq -f 13 input.bam` ; rationale being f (only in ...
ngs sam written 8 weeks ago by ctseto70 • updated 8 weeks ago by finswimmer11k
1
vote
10
answers
15k
views
10
answers
Comment: C: Assessing The Quality Of De Novo Assembled Data
... I like the Kmer approach; as an aside it can be interesting to see how much intersect() you get in Kmer spectrum between paired ends and final assemblies. Comparing the distance between PE/assembler1 and PE/assembler2 or between contigs from assembly1 and assembly2 can be quite interesting... ...
written 8 weeks ago by ctseto70
1
vote
5
answers
1.5k
views
5
answers
Comment: C: Middle author, but not first author projects. How would you approach this?
... Deeper analysis can definitely generate more useful insights; but is it enough for co-first or independent first author stuff in a wet lab? I would hope so, but unsure what the consensus is across STEM (or if there is one) ...
written 3 months ago by ctseto70
1
vote
5
answers
1.5k
views
5
answers
Comment: C: Middle author, but not first author projects. How would you approach this?
... Unsure if you can generate a publon out of putting your lab's work in context with the existing plethora of SRA datas via evaluating multiple external data sets and such, but it may be a strategy to do papers that aren't directly correlated to I-harvested-the-cells-I-first-author? ...
written 3 months ago by ctseto70
1
vote
5
answers
1.5k
views
5
answers
Comment: C: Middle author, but not first author projects. How would you approach this?
... Your comment is helpful. I think I'm still at the denial stage where I think have a chance in academia, but have yet to put together a post-doc project that is fully outside the shadow of the lab I'm in... ...
written 3 months ago by ctseto70
0
votes
0
answers
167
views
0
answers
Comment: C: WEKA and DNA analysis
... Unless there's a different weka (https://www.cs.waikato.ac.nz/ml/weka/), it's a program used for data mining, written in Java. I don't recall Weka having specific use cases for NGS though, and I'm unsure what "perfectly" means in this context. ...
written 4 months ago by ctseto70

Latest awards to ctseto

Supporter 8 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 702 users visited in the last hour