User: predeus

gravatar for predeus
predeus670
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
Answer: A: Is There A Tool To Visualize Sequence Graphs?
... 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 predeus670
0
votes
4
answers
2.0k
views
4
answers
Answer: A: Are There Any Databases/Knowledge Bases Or Other Resources Concerning Bacterial
... 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 predeus670
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 predeus670
0
votes
7
answers
1.4k
views
7
answers
Comment: C: Modern software for whole genome alignment visualization
... 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 predeus670
1
vote
2
answers
159
views
2
answers
Comment: C: Options for long-read diploid assembly
... 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 predeus670
1
vote
2
answers
159
views
2
answers
Options for long-read diploid assembly
... 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 ...
assembly diploid pacbio nanopore written 7 weeks ago by predeus670 • updated 6 weeks ago by harish130
0
votes
1
answer
668
views
1
answers
Answer: A: Reporting of multiple alignments using hisat2
... 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 predeus670
0
votes
2
answers
1.5k
views
2
answers
Comment: C: Using Hisat2 with strand specific bacteria sequences
... 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 predeus670
0
votes
1
answer
1.1k
views
1
answers
Answer: A: Gene official symbols and uncharacterised genes in the Salmonella annotations
... 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 predeus670
0
votes
3
answers
585
views
3
answers
Comment: C: Best way to assign pfam/EC/COGs to a set of proteins
... 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 predeus670

Latest awards to predeus

Student 29 days ago, asked a question with at least 3 up-votes. For Duplicates on Illumina
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
Prophet 9 months ago, created a post with more than 20 followers. For Duplicates on Illumina
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
Appreciated 21 months ago, created a post with more than 5 votes. For Duplicates on Illumina
Good Question 21 months ago, asked a question that was upvoted at least 5 times. For Duplicates on Illumina
Student 21 months ago, asked a question with at least 3 up-votes. 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?

Help
Access

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