User: mschmid

gravatar for mschmid
mschmid90
Reputation:
90
Status:
Trusted
Location:
Switzerland
Website:
http://thvd.net/
Last seen:
5 hours ago
Joined:
5 years, 6 months ago
Email:
m******@thvd.net

about me

Posts by mschmid

<prev • 86 results • page 1 of 9 • next >
0
votes
2
answers
86
views
2
answers
Comment: C: dUTP sequencing -- different strand-ratios for different samples
... Thank you. I guess it is fine now? ...
written 16 hours ago by mschmid90
1
vote
2
answers
86
views
2
answers
dUTP sequencing -- different strand-ratios for different samples
... I am analysing rna-seq data which is supposed to have strandness information via dUTP sequencing. After having mapped the Illumina data to the ref. genome using HISAT2 (applying parameter to keep strandness info) I analysed the data. I calculated the ration between the flags for plus-strand and min ...
dutp rna-seq hisat2 written 17 hours ago by mschmid90 • updated 8 hours ago by Charles Warden7.2k
0
votes
0
answers
76
views
0
answers
Comment: C: Would you remove rRNA reads in silico before testing for diff. expression?
... Hmm... just saw that it is "only" about 1.5-2%. But still not <<1% ...
written 1 day ago by mschmid90
3
votes
0
answers
76
views
0
answers
Would you remove rRNA reads in silico before testing for diff. expression?
... Hello Do some of you remove reads originating from rRNA in silico before testing for differential expression? Why or why not? Is it worth it? Or is it depending on the analysis pipeline in your opinion? My data is based on poly-A enrichment of mRNA and about 2-5% of the reads (Illumina SE 100bp) ...
rna-seq written 1 day ago by mschmid90
0
votes
0
answers
54
views
0
answers
Comment: C: Coloring nucleotide sequences according to their GC content
... The idea is, to have for example three colours: 1) Red for let's say GC below 30 and and GC above 70 2) Yellow for let's say GC below 40 and above 60 3) And rest green So the single bases (no matter if A,T,G,C) have the colour of the GC content in the current sliding window. The window could for ex ...
written 2 days ago by mschmid90
0
votes
0
answers
54
views
0
answers
Coloring nucleotide sequences according to their GC content
... Is anybody aware of a tool that does analyse the GC content of a nucleotide sequence and plot the sequence to a pdf or similar with the nucleotide sequence coloured accordingly? Ideally the tool would determine the GC content applying a sliding window approach. So the input would be a fasta or jus ...
sequence written 3 days ago by mschmid90
1
vote
1
answer
180
views
1
answers
Answer: A: ClustalO computing suboptimal alignment
... I tried MUSCLE and it seems to do a much better job. ...
written 5 months ago by mschmid90
0
votes
1
answer
180
views
1
answers
Comment: C: ClustalO computing suboptimal alignment
... Yes, MUSCLE seems to do a much better job for my application. Strange though.... ...
written 5 months ago by mschmid90
2
votes
1
answer
180
views
1
answer
ClustalO computing suboptimal alignment
... Clustal Omega - 1.2.4 I align about 600 (n) highly identical sequences. n-1 sequences are identical. There is one sequence which has some differences. For some regions I get an alignment which is obviously suboptiomal (gap is one base to early). EDIT: This is just one example. Obviously I could ju ...
alignment clustalomega written 5 months ago by mschmid90
0
votes
2
answers
173
views
2
answers
Answer: A: Where to find a list of (sequenced) WHO reference strains
... My problem is to identify/find those assemblies. Fetching them from NCBI Assemblies database is no problem. Do they have a special tag? How do I identify them? And I am still interested in a database with all WHO reference strains. ...
written 5 months ago by mschmid90

Latest awards to mschmid

Popular Question 4 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Scholar 5 months ago, created an answer that has been accepted. For A: ClustalO computing suboptimal alignment
Popular Question 6 months ago, created a question with more than 1,000 views. For Correct substitution model for yeast - RAxML
Popular Question 9 months ago, created a question with more than 1,000 views. For Correct substitution model for yeast - RAxML
Popular Question 9 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 SMRT analysis- what is difference between RS_HGAP_Assembly.2 vs RS_HGAP_Assembly.3
Supporter 9 months ago, voted at least 25 times.
Great Question 18 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 18 months ago, created a question with more than 1,000 views. For How to find pseudogenes in bacteria
Popular Question 18 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 18 months ago, created a question with more than 1,000 views. For Where to put start for assembled genome/plasmid
Popular Question 18 months ago, created a question with more than 1,000 views. For Is this mate pair insert size distribution to broad?
Popular Question 18 months ago, created a question with more than 1,000 views. For Illumina PE - what are causes for coverage drops?
Popular Question 18 months ago, created a question with more than 1,000 views. For Assemble mix of two plasmids which have partially similar sequence
Popular Question 18 months ago, created a question with more than 1,000 views. For Where to get some example metagenomics data?
Popular Question 18 months ago, created a question with more than 1,000 views. For How to get subset from NCBI databases using Accession/GI
Popular Question 18 months ago, created a question with more than 1,000 views. For Tool to detect closed contigs in FASTA/FASTQ file
Popular Question 18 months ago, created a question with more than 1,000 views. For Find telomeres and centromeres in de novo sequenced fungi
Popular Question 18 months ago, created a question with more than 1,000 views. For Blastn: In The Scoring Parameters, What Does "Linear" Mean?
Popular Question 18 months ago, created a question with more than 1,000 views. For Nice open source alternative to "contig viewer" in SeqMan Pro
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Is this mate pair insert size distribution to broad?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Where to get some example metagenomics data?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Trim Illumina PE data with trimmomatic
Popular Question 5.4 years ago, created a question with more than 1,000 views. For MiSeq: R1 vs. R2 reads show big quality difference - is that normal?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1073 users visited in the last hour