User: mschmid

gravatar for mschmid
mschmid150
Reputation:
150
Status:
Trusted
Location:
Switzerland
Website:
http://thvd.net/
Last seen:
3 weeks, 1 day ago
Joined:
5 years, 11 months ago
Email:
m******@thvd.net

about me

Posts by mschmid

<prev • 101 results • page 1 of 11 • next >
2
votes
1
answer
112
views
1
answers
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 27 days ago by mschmid150
0
votes
1
answer
115
views
1
answers
Comment: C: Which human chromosome would you use to generate a "toy data set"
... Sure, I will filter the reads. ...
written 27 days ago by mschmid150
0
votes
1
answer
115
views
1
answers
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 27 days ago by mschmid150
0
votes
1
answer
112
views
1
answers
Comment: C: Reference genome for microbiome WGS metagenomics ?
... Many samples high throughput or just a few but more in depth analysis? ...
written 27 days ago by mschmid150
4
votes
1
answer
115
views
1
answer
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 27 days ago by mschmid150
1
vote
1
answer
112
views
1
answers
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 27 days ago by mschmid150
0
votes
0
answers
137
views
0
answers
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 3 months ago by mschmid150
0
votes
0
answers
131
views
0
answers
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 3 months ago by mschmid150
0
votes
1
answer
198
views
1
answers
Comment: C: Visualize short nucleotide sequences and some ranges on top
... Sorry, just upvoted and forgot to accept. Done. ...
written 4 months ago by mschmid150
1
vote
1
answer
198
views
1
answers
Comment: C: Visualize short nucleotide sequences and some ranges on top
... THIS. IS. AWESOME. Thanks! ...
written 4 months ago by mschmid150

Latest awards to mschmid

Centurion 27 days ago, created 100 posts.
Popular Question 4 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Popular Question 9 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Scholar 10 months ago, created an answer that has been accepted. For A: ClustalO computing suboptimal alignment
Popular Question 11 months ago, created a question with more than 1,000 views. For Correct substitution model for yeast - RAxML
Popular Question 15 months ago, created a question with more than 1,000 views. For Correct substitution model for yeast - RAxML
Popular Question 15 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Popular Question 15 months ago, created a question with more than 1,000 views. For SMRT analysis- what is difference between RS_HGAP_Assembly.2 vs RS_HGAP_Assembly.3
Supporter 15 months ago, voted at least 25 times.
Great Question 24 months ago, created a question with more than 5,000 views. For MiSeq: R1 vs. R2 reads show big quality difference - is that normal?
Popular Question 24 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Popular Question 24 months ago, created a question with more than 1,000 views. For SMRT analysis- what is difference between RS_HGAP_Assembly.2 vs RS_HGAP_Assembly.3
Popular Question 24 months ago, created a question with more than 1,000 views. For Where to put start for assembled genome/plasmid
Popular Question 24 months ago, created a question with more than 1,000 views. For Is this mate pair insert size distribution to broad?
Popular Question 24 months ago, created a question with more than 1,000 views. For Illumina PE - what are causes for coverage drops?
Popular Question 24 months ago, created a question with more than 1,000 views. For Assemble mix of two plasmids which have partially similar sequence
Popular Question 24 months ago, created a question with more than 1,000 views. For Where to get some example metagenomics data?
Popular Question 24 months ago, created a question with more than 1,000 views. For How to get subset from NCBI databases using Accession/GI
Popular Question 24 months ago, created a question with more than 1,000 views. For Tool to detect closed contigs in FASTA/FASTQ file
Popular Question 24 months ago, created a question with more than 1,000 views. For Find telomeres and centromeres in de novo sequenced fungi
Popular Question 24 months ago, created a question with more than 1,000 views. For Blastn: In The Scoring Parameters, What Does "Linear" Mean?
Popular Question 24 months ago, created a question with more than 1,000 views. For Nice open source alternative to "contig viewer" in SeqMan Pro
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Is this mate pair insert size distribution to broad?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Where to get some example metagenomics data?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Trim Illumina PE data with trimmomatic

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1642 users visited in the last hour