User: mschmid

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mschmid160
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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 12 months ago by mschmid160
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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 12 months ago by mschmid160
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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 12 months ago by mschmid160
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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 12 months ago by mschmid160
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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 12 months ago by mschmid160
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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 12 months ago by mschmid160
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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 15 months ago by mschmid160
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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 15 months ago by mschmid160
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Comment: C: Visualize short nucleotide sequences and some ranges on top
... Sorry, just upvoted and forgot to accept. Done. ...
written 15 months ago by mschmid160
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Comment: C: Visualize short nucleotide sequences and some ranges on top
... THIS. IS. AWESOME. Thanks! ...
written 15 months ago by mschmid160

Latest awards to mschmid

Popular Question 11 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Centurion 12 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Popular Question 21 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
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Supporter 2.2 years ago, voted at least 25 times.
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Popular Question 3.6 years ago, created a question with more than 1,000 views. For Where to get some example metagenomics data?

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