User: predeus

gravatar for predeus
predeus1.2k
Reputation:
1,250
Status:
Trusted
Location:
Russia
Website:
https://bioinf.me/en/r...
Twitter:
APredeus
Scholar ID:
Google Scholar Page
Last seen:
3 days, 22 hours ago
Joined:
7 years ago
Email:
p******@gmail.com

about me

Posts by predeus

<prev • 148 results • page 1 of 15 • next >
0
votes
1
answer
141
views
1
answers
Answer: A: Trinity RSEM Bowtie2 align_and_estimate_abundance script error
... 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 8 weeks ago by predeus1.2k
2
votes
1
answer
250
views
1
answers
Answer: A: Sequence duplication levels in de-novo assemblies
... 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 8 weeks ago by predeus1.2k
0
votes
2
answers
226
views
2
answers
Answer: A: Principal Component Analysis PCA
... 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 8 weeks ago by predeus1.2k
0
votes
2
answers
226
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 8 weeks ago by predeus1.2k
1
vote
2
answers
2.0k
views
2
answers
Answer: A: Best strategy to get GO terms for a proteome?
... In case somebody is searching this: newest version of InterProScan works very nicely and adds GO terms as well as Reactome pathways to the annotation based on discovered domains. Of course, these approaches have a bunch of limitations, but still - I think this is the easiest way to do it. Took me ab ...
written 8 weeks ago by predeus1.2k
0
votes
0
answers
200
views
0
answers
Comment: C: Eukaryotic gene annotation on gene predictions
... Wow, thank you. It takes a little while to get InterProScan running, but once you got it going, it's quite.. impressive. ...
written 8 weeks ago by predeus1.2k
0
votes
0
answers
200
views
0
answers
Comment: C: Eukaryotic gene annotation on gene predictions
... Thank you, I'll give it a shot. ...
written 3 months ago by predeus1.2k
4
votes
0
answers
200
views
0
answers
Eukaryotic gene annotation on gene predictions
... Hello all, I was wondering if there is a good tool for annotation of eukaryotic genes obtained by gene prediction, for example, by Braker pipeline (or any other gene prediction pipeline for that matter)? By annotation I mean basically blasting and hmm-scanning putative proteins against various dat ...
annotation gene prediction eukaryotic written 3 months ago by predeus1.2k • updated 8 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
1.6k
views
0
answers
Comment: C: RepeatModeler finishes without creating output files
... In case somebody is looking through this: it was a bug and it was fixed. The current version works OK. ...
written 3 months ago by predeus1.2k
0
votes
2
answers
1.8k
views
2
answers
Answer: A: RepeatMasker on new species
... Does anybody know how crucial it is to use your own repeat library in order to successfully mask repeats? I know it would depend on species, of course. Is there much difference in the amount of sequence masked? Thank you for any input. ...
written 3 months ago by predeus1.2k

Latest awards to predeus

Great Question 25 days ago, created a question with more than 5,000 views. For Find All Annotated Rrna (Rdna) Sequences
Popular Question 28 days ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Popular Question 5 weeks ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Prophet 10 weeks ago, created a post with more than 20 followers. For Modern software for whole genome alignment visualization
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For Get a complete GSM-to-SRX/SRR table
Voter 3 months ago, voted more than 100 times.
Appreciated 3 months ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 3 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Appreciated 4 months ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For Get a complete GSM-to-SRX/SRR table
Appreciated 5 months ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Guru 5 months ago, received more than 100 upvotes.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Scholar 5 months ago, created an answer that has been accepted. For A: Programs for bacterial gene prediction/annotation for nanopore assembly?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Epic Question 7 months ago, created a question with more than 10,000 views. For Duplicates on Illumina
Popular Question 8 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Great Question 10 months ago, created a question with more than 5,000 views. For Duplicates on Illumina
Centurion 11 months ago, created 100 posts.
Librarian 12 months ago, created a post with more than 10 bookmarks. For Duplicates on Illumina
Popular Question 12 months ago, created a question with more than 1,000 views. For Get a complete GSM-to-SRX/SRR table
Student 13 months ago, asked a question with at least 3 up-votes. For Duplicates on Illumina

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1843 users visited in the last hour