User: onestop_data

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onestop_data260
Reputation:
260
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Website:
https://onestopdataana...
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onestop_data
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6 hours ago
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4 months, 1 week ago
Email:
g****************@gmail.com

Bioinformatics scientist and blogger talking about Bioinformatics and Data analysis. 

Posts by onestop_data

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Multiple sequence alignment clean-up
... Try running it with the flag --remove_ambiguous ...
written 5 weeks ago by onestop_data260
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Answer: A: Multiple sequence alignment clean-up
... 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 weeks ago by onestop_data260
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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 8 weeks ago by onestop_data260
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Answer: A: Binning tools for metagenomics
... [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 8 weeks ago by onestop_data260
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Answer: A: metabat installation problem with conda
... 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 10 weeks ago by onestop_data260
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Answer: A: Genome size estimation using Kmergenie
... 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 11 weeks ago by onestop_data260
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Answer: A: Cross assembly of metagenomics
... 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 11 weeks ago by onestop_data260
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Answer: A: Reads Simulation and Read Simulator
... 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 3 months ago by onestop_data260
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Answer: A: Paired-end metagenomics data for MEGAN analysis
... 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 3 months ago by onestop_data260
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Answer: A: MetaBat 2 does not produce a bin while running ok
... 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 3 months ago by onestop_data260

Latest awards to onestop_data

Scholar 5 weeks ago, created an answer that has been accepted. For A: Searching for genes in assembles genome database
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Multiple sequence alignment clean-up
Rising Star 11 weeks ago, created 50 posts within first three months of joining.
Scholar 4 months ago, created an answer that has been accepted. For A: Searching for genes in assembles genome database
Scholar 4 months ago, created an answer that has been accepted. For A: Searching for genes in assembles genome database
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.

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