User: predeus
predeus • 670
- Reputation:
- 670
- Status:
- Trusted
- Location:
- Russia
- Website:
- http://bioinf.me/research
- Twitter:
- APredeus
- Scholar ID:
- Google Scholar Page
- Last seen:
- 17 hours ago
- Joined:
- 5 years, 11 months ago
- Email:
- p******@gmail.com
about me
Posts by predeus
<prev
• 94 results •
page 1 of 10 •
next >
1
vote
3
answers
3.0k
views
3
answers
... Old post, but just for the sake of modern searches: [Bandage](https://github.com/rrwick/Bandage) is very good modern tool with lot's of good functionality ...
written 17 hours ago by
predeus • 670
0
votes
4
answers
2.0k
views
4
answers
... A nice up-to-date collection of databases is available in abricate: https://github.com/tseemann/abricate
Otherwise, it's mostly blasting against databases for every such tool. ...
written 23 days ago by
predeus • 670
2
votes
4
answers
2.1k
views
4
answers
Answer:
A: Bacterial GWAS analysis?
... Here's a nice review that mentions many important papers in bacterial GWAS, and does a pretty good job explaining the difference between human GWAS and various attempts to do this in bacteria.
https://figshare.com/articles/The_background_of_bacterial_GWAS/5550037 ...
written 23 days ago by
predeus • 670
0
votes
7
answers
1.4k
views
7
answers
... Nothing outside what was mentioned here, no.
This tool was useful: https://dnanexus.github.io/dot/
it uses Nucmer alignments and creates a pretty useful visualization. ...
written 6 weeks ago by
predeus • 670
1
vote
2
answers
159
views
2
answers
... Not just long reads - there's plenty of assemblers for that (and, no offence, but I would not rank the options you mentioned too highly - miniasm-racon is way faster, and Flye and Canu a a lot more user friendly and generate better results). However, I was interested in tools specifically geared tow ...
written 7 weeks ago by
predeus • 670
1
vote
2
answers
159
views
2
answers
... Hello all,
I was wondering about the options for ploidy-aware assemblers for long reads. I know there is FALCON-unzip for Pacbio, and I also have seen a [recent preprint][1]. What are other options for highly heterozygous genomes? Thank you in advance!
[1]: https://www.biorxiv.org/content/earl ...
0
votes
1
answer
668
views
1
answers
... This is actually one of the most confusing things about alignment in general.
What this description means (I think) is that if you have -k set to 10, and aligner will find 10 locations where the read aligns with a certain mapping score, it will report them and stop looking further.
What I do not ...
written 11 weeks ago by
predeus • 670
0
votes
2
answers
1.5k
views
2
answers
... There's an interesting caveat I just discovered. Apparently, bwa and bowtie2 do not add NH tag to the resulting SAM/BAM files (that's the flag indicating how many times did this particular read ID was reported mapped - so, simply put, it's important to keep track of the multimapping reads).
So, an ...
written 11 weeks ago by
predeus • 670
0
votes
1
answer
1.1k
views
1
answers
... Unfortunately, it is never safe to assume such things with bacterial gene names.
In your own list, SL0471 is identified as aefA - this should be its name, unless there's one that is used more often.
SL identifiers are from SL1344 strain. You can take another 10-20 reference strains from NCBI and ...
written 12 weeks ago by
predeus • 670
0
votes
3
answers
585
views
3
answers
... This is basically a bacterial pan-genome - all the predicted proteins, with 100% redundant proteins removed, but not more - I'm experimenting with species-specific paralog discrimination.
It's quite massive and would have lots and lots of hits with nr, I am sure. ...
written 3 months ago by
predeus • 670
Latest awards to predeus
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For Classify Genes As Expressed Or Not Expressed
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Too late to switch to Bioinformatics?
Appreciated
4 months ago,
created a post with more than 5 votes.
For C: How To Convert Gencode Gtf Into Bed Format ?
Great Question
5 months ago,
created a question with more than 5,000 views.
For Duplicates on Illumina
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Get a complete GSM-to-SRX/SRR table
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Commentator
18 months ago,
created a comment with at least 3 up-votes.
For C: How To Convert Gencode Gtf Into Bed Format ?
Supporter
19 months ago,
voted at least 25 times.
Popular Question
21 months ago,
created a question with more than 1,000 views.
For How To Determine If Library Is Strand-Specific
Good Question
21 months ago,
asked a question that was upvoted at least 5 times.
For Duplicates on Illumina
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Find All Annotated Rrna (Rdna) Sequences
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For How To Determine If Library Is Strand-Specific
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For Find All Annotated Rrna (Rdna) Sequences
Teacher
4.4 years ago,
created an answer with at least 3 up-votes.
For A: Too late to switch to Bioinformatics?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 735 users visited in the last hour