User: onestop_data
onestop_data • 260
- Reputation:
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- https://onestopdataana...
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- onestop_data
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Bioinformatics scientist and blogger talking about Bioinformatics and Data analysis.
Posts by onestop_data
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... Try running it with the flag --remove_ambiguous ...
written 5 months ago by
onestop_data • 260
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... Hi - this script was re-written using pysam and should do what you want. Just make sure you pass the flag **--keep_all_duplicates**
https://onestopdataanalysis.com/clean-fasta-fastq-file/ ...
written 5 months ago by
onestop_data • 260
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Comment:
C: Binning tools for metagenomics
... great point, but it is important to remember that it is a metagenomic dataset, so there is not enough coverage to recover the full genome, thus the complement is low for many of the bins.
I have added some extra words to the conclusion to make it more clear. thanks
...
written 6 months ago by
onestop_data • 260
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... [Please check this out.][1] Here I describe in details how to use [CONCOT][2] and [Metabat][3]
[1]: https://onestopdataanalysis.com/binning/
[2]: http://%20https://onestopdataanalysis.com/binning/
[3]: https://onestopdataanalysis.com/binning/ ...
written 6 months ago by
onestop_data • 260
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... How are you installing it with conda? are you activating the bioconda channel?
Please check section 2. (https://bioconda.github.io/user/install.html#install-conda) ...
written 6 months ago by
onestop_data • 260
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... Yes, you can!
KmerGenie can be used to estimate the genome size or the best k-mer length to assemble your data. [I have written a blog post on how to install and use KmerGenie.][1]
[1]: https://onestopdataanalysis.com/estimate-genome-size-best-k-mer-size-for-assembly/ ...
written 6 months ago by
onestop_data • 260
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... CrAss was designed for comparative metagenomics. You assemble all your metagenomes together, and the tool leverages the overlapping across samples to infer the distance within samples.
The tool first required an ACE file, but this not common anymore (I think MIRA assembler generated it as one of it ...
written 6 months ago by
onestop_data • 260
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... I have written this [tutorial][1] on how to simulate reads for single-cell genomes and metagenomics. It covers how to simulate Illumina (NovaSeq, HiSeq or MiSeq), Pacific Biosciences (PacBio) SMRT, and Oxford Nanopore reads.
https://onestopdataanalysis.com/read-simulator/
[1]: https://onestopda ...
written 7 months ago by
onestop_data • 260
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... I think merging the pair-ends is a good idea so you can guarantee long reads, and thus better resolution when working on the taxonomic and functional analysis. That is what [SUPER-FOCUS recommends][1] when running the functional analysis.
Do you have a tool to merge your pair ended reads? [PEAR][2] ...
written 7 months ago by
onestop_data • 260
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... I guess it means that Metabat2 somehow was not able to bin any of your contigs. What did you use to create your BAM files prior to running it? did you make sure it was a sorted BAM?
I ran the tool today on a simulated dataset with 10 species, and it was only able to bin 2 of them. I guess in your c ...
written 7 months ago by
onestop_data • 260
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