Moderator: 5heikki

gravatar for 5heikki
5heikki7.8k
Reputation:
7,800
Status:
Trusted
Location:
Finland
Last seen:
40 minutes ago
Joined:
4 years, 12 months ago
Email:
h***************@gmail.com

about me

Posts by 5heikki

<prev • 1,064 results • page 1 of 107 • next >
0
votes
1
answer
121
views
1
answers
Comment: C: Don't understand the assignment - Artemis
... Perhaps you're supposed to compare the ORF annotations, percent that intersect, percent unique to either method, etc. ...
written 26 days ago by 5heikki7.8k
1
vote
0
answers
126
views
0
answers
Comment: C: standalone blast output to excel
... Yes, just use `-outfmt 6` or `-outfmt 10` for tab or comma separated values and import to excel accordingly. You also need to define the output fields you're interested in. You can see all options with `blastn -help` ...
written 29 days ago by 5heikki7.8k
1
vote
1
answer
84
views
1
answers
Answer: A: Is there a database of phylogenetic information?
... You mean like Silva's [Living Tree][1]? [1]: https://www.arb-silva.de/projects/living-tree/ ...
written 4 weeks ago by 5heikki7.8k
0
votes
4
answers
944
views
4
answers
Comment: C: Misunderstood parameter of NCBI BLAST
... Yeah, but the option is basically useless as it is. Like, in what kind of use case would the output make sense? Why not have an option `-max_random_hits` while at it.. ...
written 5 weeks ago by 5heikki7.8k
3
votes
0
answers
184
views
0
answers
Comment: C: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does
... My bad for not noticing the previous posts. Anyway, I think this issue deserves a lot of visibility. Like one of those previous posts could be a sticky until NCBI does something about it.. ...
written 5 weeks ago by 5heikki7.8k
4
votes
0
answers
184
views
0
answers
News: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does
... > To our surprise, we have recently discovered that this intuition is incorrect. Instead, BLAST returns the first N hits that exceed the specified E-value threshold, which may or may not be the highest scoring N hits. The invocation using the parameter "-max_target_seqs 1" simply returns the firs ...
software error news blast written 5 weeks ago by 5heikki7.8k • updated 5 weeks ago by Devon Ryan86k
0
votes
2
answers
275
views
2
answers
Comment: C: Workstation : More RAM or Faster RAM
... What's enough RAM though? This week I noticed that 256GB isn't enough RAM for e.g. indexing a large reference with default Bowtie2 settings. Sure I can increase offrate but it goes directly against my aims.. ...
written 5 weeks ago by 5heikki7.8k
0
votes
1
answer
330
views
1
answers
Comment: C: Missing sequences in local NT database
... Did you create it with the `parse_seqids` flag? I recall it taking way longer than a few hours. The compression part shouldn't take that long since it can be parallelized ...
written 5 weeks ago by 5heikki7.8k
1
vote
0
answers
97
views
0
answers
Comment: C: primers for whole metagenome
... It's a step you perform prior to any sequencing ...
written 5 weeks ago by 5heikki7.8k
0
votes
0
answers
97
views
0
answers
Comment: C: primers for whole metagenome
... This is not a bioinformatics question. Anyway, buy some multiple displacement amplification kit ([just be aware of its shortcomings][1]).. [1]: https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-3 ...
written 6 weeks ago by 5heikki7.8k

Latest awards to 5heikki

Scholar 16 days ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Popular Question 25 days ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Script for extracting data from a tab-delimited file
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Popular Question 4 months ago, created a question with more than 1,000 views. For Bootsrapped tree from a distance matrix
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 6 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 7 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1775 users visited in the last hour