User: willnotburn

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willnotburn20
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United States, Michigan State Universtiy
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1 year ago
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Posts by willnotburn

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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 5 days ago by willnotburn20
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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 10 days ago by willnotburn20
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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 10 days ago by willnotburn20
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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 13 days ago by willnotburn20
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Comment: C: metagenomic assembly has low coverage; what are my options?
... Is there harm in going too low on the trimming cutoff score? Would the aligner, like `bowtie2`, be able to discard bad reads that wouldn't align well? ...
written 13 days ago by willnotburn20
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Comment: C: metagenomic assembly has low coverage; what are my options?
... It was a HiSeq Rapid SBS Kit V2 dual-flow cell paired-end 250. The page you liked says **greater than 75% of bases above Q30 at 2 × 250 bp**. The reverse reads were a little shotty. The enzyme probably died early. Alas, I no longer have the DNA samples for additional sequencing. ...
written 13 days ago by willnotburn20
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Comment: C: metagenomic assembly has low coverage; what are my options?
... Thanks, @h.mon! I haven't considered going as low as 10 cutoff on trimming. According to `FastQC`, excellent quality is >28 and good quality is >20. Maybe I'll try 20 first. Indeed, with the cutoff at 30, I'm discarding about 73% of my seqs. Also, I'll try to use --very-sensitive-local flag i ...
written 13 days ago by willnotburn20
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metagenomic assembly has low coverage; what are my options?
... My metagenomic assembly has low coverage. What upstream steps can I adjust to increase coverage? At what possible cost? Low coverage of metagenomic assemblies must be a common problem, but I've been unable to find a "quick start guide" i.e. an outline of recommendations to remedy this, barring "do m ...
assembly trimming metagenomic coverage megahit written 13 days ago by willnotburn20 • updated 13 days ago by h.mon13k
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Answer: A: map both interleaved and orphaned reads to assembly for each sample (with bowtie
... Thanks to @genomax and some trial and error, I figured this one out. `bowtie2` can absolutely map both paired and unpaired (orphaned) reads at the same time. The key is to supply paired reads as separate forward and reverse inputs, as opposed to an interleaved file. This works: `bowtie2 -x final.c ...
written 17 days ago by willnotburn20
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Comment: C: map both interleaved and orphaned reads to assembly for each sample (with bowtie
... Thanks, @genomax!! Your answer works and may be the most straightforward option. I am still holding out for a `bowtie2` solution, perhaps mediated by `samtools`. The only reason is my amateur understanding of `bbmap` performance ([large false positive rate][1]). [1]: http://merenlab.org/2015/06 ...
written 21 days ago by willnotburn20

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Scholar 17 days 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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