User: mschmid

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mschmid150
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Posts by mschmid

<prev • 101 results • page 1 of 11 • next >
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Answer: A: Reference genome for microbiome WGS metagenomics ?
... If you have many samples, want to do an in depth analysis and have enough time I personally would do the following: 1) Get a basic set of RefSeq or Ensembl Bacterial genome assemblies covering all taxonomic groups. Either take all of them or perform a clever sub setting (like taking representative ...
written 5 months ago by mschmid150
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Comment: C: Which human chromosome would you use to generate a "toy data set"
... Sure, I will filter the reads. ...
written 5 months ago by mschmid150
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Comment: C: Which human chromosome would you use to generate a "toy data set"
... Sure, forgot to state the goal. It is more about mapping short reads and not about genes. So this is not a problem. ...
written 5 months ago by mschmid150
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Comment: C: Reference genome for microbiome WGS metagenomics ?
... Many samples high throughput or just a few but more in depth analysis? ...
written 5 months ago by mschmid150
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Which human chromosome would you use to generate a "toy data set"
... I have to generate a "toy dataset" with one human chromosome and short reads mapping on these contigs. Which one would you pick? I would go for chromosome 21 since: 1) it is short, so less data 2) it has no gender bias (depth) like X/Y chromosome. Is this a good pick or would you advise to go for ...
genome sequencing written 5 months ago by mschmid150
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Comment: C: Reference genome for microbiome WGS metagenomics ?
... What do you want to achieve? What kind of samples do you have? You can also subset NCBI/Ensembl databases if you have specific targets or can exclude specific bacteria. Like this you can have a high resolution for you target group. EDIT: Another strategy is to pre-screen your data with a subset of ...
written 5 months ago by mschmid150
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Mimicing the Blastn "lineage report" from online Blast service
... Does anyone know a good way to mimic the the "lineage report" from online Blastn results? I am talking about this here: ![Blast lineage report][1] [1]: https://cdn1.imggmi.com/uploads/2019/10/31/bc83a21fa5c1bc376b6ddefcd060dca5-full.png ...
blast written 8 months ago by mschmid150
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How to get all Blastn hits
... I am performing the following workflow: 1. I start with a bunch of nucleotide sequences as a FASTA 2. I blast them against a custom blast database using standalone blastn (`-task blastn`) 3. Then I cut out all the blastn hits from the initial FASTA nucleotide sequences. This leaves me with supposed ...
blastn written 8 months ago by mschmid150
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Comment: C: Visualize short nucleotide sequences and some ranges on top
... Sorry, just upvoted and forgot to accept. Done. ...
written 8 months ago by mschmid150
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Comment: C: Visualize short nucleotide sequences and some ranges on top
... THIS. IS. AWESOME. Thanks! ...
written 8 months ago by mschmid150

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