User: predeus
predeus • 1.3k
- Reputation:
- 1,290
- Status:
- Trusted
- Location:
- Russia
- Website:
- https://bioinf.me/en/r...
- Twitter:
- APredeus
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 week, 6 days ago
- Joined:
- 7 years, 3 months ago
- Email:
- p******@gmail.com
about me
Posts by predeus
<prev
• 154 results •
page 1 of 16 •
next >
0
votes
7
answers
5.6k
views
7
answers
... Pretty much nothing outside things mentioned above. Dot is very good for large-scale comparison, and Artemis Comparison Tool (ACT) works nicely for detailed comparison using GFF annotation. ...
written 4 weeks ago by
predeus • 1.3k
0
votes
0
answers
100
views
0
answers
... The BAM file still needs to be sorted, and AFAIK there are slightly different requirements for paired-end (fragment) and single-end (read) quantification. Basically, featureCounts will try to fix the mate pairs if it detects inconsistencies, but it's much slower than actual read counting, so it's be ...
written 6 weeks ago by
predeus • 1.3k
0
votes
2
answers
1.3k
views
2
answers
... It seems like MetaMaps should be quite good for this task. I'm about to test it with a couple of my datasets. ...
written 6 weeks ago by
predeus • 1.3k
0
votes
1
answer
142
views
1
answers
... Thank you, that's an interesting approach. I need to compare quite distant species though, so I don't think alignment in nucleotide space would be very useful. ...
written 9 weeks ago by
predeus • 1.3k
2
votes
1
answer
142
views
1
answer
... Hello all,
I was wondering if you know of a good tutorial showing how to make a simple phylogeny of several eukaryotic species?
Basically, as far as I understand, you start with an annotated genome, and need to 1) identify single-copy orthologues; 2) do multiple alignment; 3) select the "good" p ...
0
votes
0
answers
665
views
0
answers
... Did you gather any useful knowledge about the best way to use 10X reads? All the software I've tried seems to act up. ...
written 12 weeks ago by
predeus • 1.3k
0
votes
1
answer
209
views
1
answers
... Dir paths look kind of funny. Did you try running the commands mentioned in the debug manually?
Try checking what "Trinity.fasta.bowtie2" actually is - is this a wrapper script? ...
written 5 months ago by
predeus • 1.3k
2
votes
1
answer
304
views
1
answers
... You probably would want to map the reads back to the assembly and then evaluate sequence duplication. FastQC works with raw reads and has limited power to inform you about the nature of your problems.
If after paired-end mapping you still get high duplication rate, you probably are dealing with PC ...
written 5 months ago by
predeus • 1.3k
0
votes
2
answers
282
views
2
answers
... I'd also like to add that if 80% of variance in your 20-sample RNA-seq PCA is explained by PC1, there's either something very wrong with your samples, or with the way you are analyzing your data. Make sure they are log-transformed and normalized - ideally with something like vst or rlog transformati ...
written 5 months ago by
predeus • 1.3k
0
votes
2
answers
282
views
2
answers
Comment:
C: Principal Component Analysis PCA
... They must have only ran it on SNPs :) basically, the number of PCs = number of rows.
Rows could be genes (for RNA-seq), SNPs, or anything else. ...
written 5 months ago by
predeus • 1.3k
Latest awards to predeus
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Programs for bacterial gene prediction/annotation for nanopore assembly?
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For Does any large resequencing project have a genuinely hg38 VCF?
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For Does any large resequencing project have a genuinely hg38 VCF?
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Too late to switch to Bioinformatics?
Great Question
3 months ago,
created a question with more than 5,000 views.
For How To Determine If Library Is Strand-Specific
Great Question
4 months ago,
created a question with more than 5,000 views.
For Find All Annotated Rrna (Rdna) Sequences
Popular Question
4 months ago,
created a question with more than 1,000 views.
For PCA and DE analysis for loop design microarray
Popular Question
4 months ago,
created a question with more than 1,000 views.
For PCA and DE analysis for loop design microarray
Prophet
5 months ago,
created a post with more than 20 followers.
For Modern software for whole genome alignment visualization
Good Question
6 months ago,
asked a question that was upvoted at least 5 times.
For Get a complete GSM-to-SRX/SRR table
Voter
6 months ago,
voted more than 100 times.
Appreciated
6 months ago,
created a post with more than 5 votes.
For C: How To Convert Gencode Gtf Into Bed Format ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For PCA and DE analysis for loop design microarray
Appreciated
7 months ago,
created a post with more than 5 votes.
For C: How To Convert Gencode Gtf Into Bed Format ?
Good Question
7 months ago,
asked a question that was upvoted at least 5 times.
For Get a complete GSM-to-SRX/SRR table
Appreciated
9 months ago,
created a post with more than 5 votes.
For C: How To Convert Gencode Gtf Into Bed Format ?
Guru
9 months ago,
received more than 100 upvotes.
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Too late to switch to Bioinformatics?
Student
9 months ago,
asked a question with at least 3 up-votes.
For Version history and design files for exome kits from Agilent, Roche(Nimblegen), and Illumina
Scholar
9 months ago,
created an answer that has been accepted.
For A: Programs for bacterial gene prediction/annotation for nanopore assembly?
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Too late to switch to Bioinformatics?
Epic Question
10 months ago,
created a question with more than 10,000 views.
For Duplicates on Illumina
Popular Question
12 months ago,
created a question with more than 1,000 views.
For PCA and DE analysis for loop design microarray
Student
14 months ago,
asked a question with at least 3 up-votes.
For Version history and design files for exome kits from Agilent, Roche(Nimblegen), and Illumina
Great Question
14 months ago,
created a question with more than 5,000 views.
For Duplicates on Illumina
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1474 users visited in the last hour