User: willnotburn

gravatar for willnotburn
willnotburn40
Reputation:
40
Status:
New User
Location:
United States, Michigan State Universtiy
Last seen:
6 months, 1 week ago
Joined:
3 years, 4 months ago
Email:
w**********@gmail.com

Posts by willnotburn

<prev • 22 results • page 1 of 3 • next >
0
votes
0
answers
191
views
0
answers
Forum: MAGs annotation tools: prokka vs eggnog
... Are there any obvious advantages/disadvantages to using one over the other? Both use HMM (I think), both are hierarchical (starting with EggNOG 4.5). Are they simply competitors? Perhaps there is a trade-off between database size and the quality of curation. Is one of them larger than the other on t ...
genome annotation forum written 6 months ago by willnotburn40
1
vote
1
answer
904
views
1
answer
Parse NCBI XML sample information into a data frame in R
... There are packages out there that manipulate XML in R. But I've spent two full days and have largely given up. There must be an existing tool to simply take a downloaded sample metadata file (for all samples in an NCBI project) from NCBI (xml format) and convert it into a data frame in R. No search ...
ncbi R xml written 17 months ago by willnotburn40
0
votes
1
answer
1.4k
views
1
answers
Comment: C: assemblers choose high k-mers: what does that mean?
... Thanks, genomax. A lot in 1st and 3rd papers is - and will likely always be - outside of my field. But I am happy to have gleaned one thing from your second bullet point. If the best k-mer length is often 80% of read length, then the longest available k-mer (141 for `megahit` and 127 for `metaSPAde ...
written 2.1 years ago by willnotburn40
3
votes
1
answer
1.4k
views
1
answer
assemblers choose high k-mers: what does that mean?
... I am co-assembling metagenomic PE reads. `megahit`and `metaSPAdes`consistently choose the final assembly as one based on the longest k-mer (141). What does that tell about my input data and the assembly? Any cause for joy or concern? ...
assembly metagenomic written 2.1 years ago by willnotburn40
0
votes
0
answers
766
views
0
answers
What to do with unpaired reads post-trimming?
... After `Trimmomatic`, I am left with a large number of unpaired (orphaned) reads. Are they ultimately useful? I could include them for assembly with `megahit`. But a few downstream tools don't deal well with mapping and/or counting orphaned reads, notably `htseq`. So, does it make sense to assemble ...
de-novo htseq trimming metagenomic mapping written 2.3 years ago by willnotburn40
0
votes
0
answers
1.5k
views
0
answers
Comment: C: Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
... It is very feasible for 16s to be identical between your bins. [E.coli and Shigella][1] - different species - apparently, have nearly identical 16s. In the oceans, all Prochlorococcus strains - from the entire planet, all ocean depths, low and high light types - are within 97% similarity. I'm not sa ...
written 2.3 years ago by willnotburn40
2
votes
0
answers
1.5k
views
0
answers
Comment: C: Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
... 1. [CheckM][1] has an SSU finder option. I do not know the under-the-hood of the source code and whether it's "sensitive". 2. What do the other single-copy markers look like? Are they identical, too? [1]: http://%20https://github.com/Ecogenomics/CheckM/wiki/Utility-Commands ...
written 2.3 years ago by willnotburn40
0
votes
0
answers
667
views
0
answers
metagenomic assembly coverage, for multiple samples
... I have multiple samples (interleaved reads), which were co-assembled into one `final.contigs.fa` assembly. The downstream goal is analysis of gene distribution among the samples, multivariate stats etc. To do that, the first step is to map reads from each sample back onto `final.contigs.fa` with `bo ...
bowtie2 metagenomics samtools coverage mpileup written 2.3 years ago by willnotburn40
0
votes
1
answer
893
views
1
answers
Comment: C: metagenomic assembly has low coverage; what are my options?
... I played around with re-trimming. What seems to have made the most difference is the MINLEN parameter. I used to have it set at 135, which I thought was fine for a 250 kit. Changing it to 50 now gives me >90% of reads passing the filter. ...
written 2.3 years ago by willnotburn40
0
votes
2
answers
1.4k
views
2
answers
Answer: A: shotgun metagenomic data analysis
... You want [Phylosift][1], developed by Jon Eisen's group at UC Davis. There's a pretty great tutorial (by an unrelated group) on it [here][2], which also includes many other downstream analyses you may to pursue in the future. [1]: https://phylosift.wordpress.com/tutorials/running-phylosift/phylo ...
written 2.3 years ago by willnotburn40

Latest awards to willnotburn

Popular Question 17 months ago, created a question with more than 1,000 views. For assemblers choose high k-mers: what does that mean?
Scholar 2.3 years ago, created an answer that has been accepted. For A: map both interleaved and orphaned reads to assembly for each sample (with bowtie

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1582 users visited in the last hour