User: willnotburn

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willnotburn40
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Location:
United States, Michigan State Universtiy
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2 weeks ago
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1 year, 3 months ago
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Posts by willnotburn

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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 26 days ago by willnotburn40
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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 26 days ago by willnotburn40
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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 11 weeks ago by willnotburn40
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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 12 weeks ago by willnotburn40
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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 12 weeks ago by willnotburn40
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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 12 weeks ago by willnotburn40
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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 3 months ago by willnotburn40
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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 3 months ago by willnotburn40
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best CDS prediction tool for online annotation submission
... I would like to annotate a metagenomic assembly with KEGG using the [GhostKOALA][1] service. The assembly was produced with `megahit` and is in FASTA format. `GhostKOALA` requires amino acid `.faa` files as input. **Question**: what's the best tool to translate the assembly? I'm thinking to use [pr ...
fasta annotation ghostkoala prodigal cds written 3 months ago by willnotburn40
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Comment: C: metagenomic assembly has low coverage; what are my options?
... An idea that incorporates @h.mon's comments! How about 1. Make the reference assembly with high quality (>Q30) reads (using `megahit`) 2. Get coverage information (using `bowtie2`) by mapping an increased number of reads by dropping quality cutoff to >Q20 My current assembly, made with >Q ...
written 3 months ago by willnotburn40

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Scholar 3 months ago, created an answer that has been accepted. For A: map both interleaved and orphaned reads to assembly for each sample (with bowtie

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