User: Graslevy

gravatar for Graslevy
Graslevy240
Reputation:
240
Status:
Trusted
Location:
UK
Last seen:
2 years, 7 months ago
Joined:
7 years, 9 months ago
Email:
g*******@aol.co.uk

Posts by Graslevy

<prev • 35 results • page 1 of 4 • next >
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Performance of circRNA detection tools
... I agree with you. The CIRI authors mention memory consumption ~20% of the size of the SAM file. I find that this is not the case. For a SAM file of about 135GB, it is currently using up to 70GB of RAM and was halted overnight on a node with 100GB of RAM. It is a good tool, but the memory consumptio ...
written 3.6 years ago by Graslevy240
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Performance of circRNA detection tools
... Hello Geek_y,  I have generated simulated data from 4500 published circRNAs. CIRI found most of the structures with up to 125 false positives (structures not expected). I have linked some of the FASTQ data for anyone to re-analyse, I can send more privately. ...
written 3.6 years ago by Graslevy240
6
votes
0
answers
2.7k
views
0
answers
Performance of circRNA detection tools
... Hey Guys, Using simulated data, I have compared 2 recent methods for identifying circRNAs, CIRI & CIRCexplorer (tophat fusion version). I find both to have weird behaviors and would like to know reasons for these. Firstly, simulated data was generated from previously identified structures in c ...
circrna rna-seq written 3.6 years ago by Graslevy240 • updated 3.5 years ago by Biostar ♦♦ 20
0
votes
1
answer
914
views
1
answers
Answer: A: Resolving Protein Identification Conflicts
... I acknowledge there is no easy solution to this problem and some conflicts will persist. I had to choose between using a supervised learning solution (the one described in the question) and a soft classifier (as previously described by others including PeptideProphet). I ended up implementing an exp ...
written 5.0 years ago by Graslevy240
0
votes
1
answer
914
views
1
answer
Resolving Protein Identification Conflicts
... Hey Guys, I am trying to solve the problem of resolving protein identification conflicts. After searching Mascot to identify peptides, some peptides are often identified as evidence for various/multiple proteins (some due to homology, others due to errors in DB); the task is to resolve such conflict ...
proteomics written 5.0 years ago by Graslevy240
0
votes
0
answers
1.7k
views
0
answers
Comment: C: Creating A Bioinformatics Support Unit
... Hello Casey, I understand the reasons for closing my last post. However, although the topics are similar, this post requests details pertaining to the logistics of creating a BSU not the personnel required. Perhaps the title can be changed leaving the post open. I do sincerely need answers to thes ...
written 6.0 years ago by Graslevy240
0
votes
1
answer
3.4k
views
1
answers
Answer: A: Using Cuffdiff With Merged Transcripts (Cuffmerge-Merge.Gtf)
... As you can see from the usage example on Cufflinks page,: cuffdiff [options]* transcripts.gtf sample1_replicate1.sam[,...,sample1_replicateM]> your merge.gtf file will replace transcripts.gtf. You may also need to convert to SAM output or request SAM during tophat run. ...
written 6.0 years ago by Graslevy240
0
votes
0
answers
1.7k
views
0
answers
Comment: C: Creating A Bioinformatics Support Unit
... Yes. My apologies for not making that clear.. ...
written 6.0 years ago by Graslevy240
2
votes
0
answers
1.7k
views
8 follow
0
answers
(Closed) Creating A Bioinformatics Support Unit
... Hey Guys, I am hoping to get informed responses (and personal experiences) relating to the logistics of setting up a BSU. This unit will analyse RNA-Seq, Microarray, GWAS and Exome sequencing data. Please advise on cost, linux cluster set-up and other hardware. Any advise on marketing strategies ...
clustering written 6.0 years ago by Graslevy240
3
votes
4
answers
3.2k
views
4
answers
Answer: A: How One Can Computationally Analyse The Functional Impact Of Frameshift Mutation
... To bolster Larry's answer, in the case of pre-mature STOP codons, three things are likely to happen: 1. Non-mediated decay (NMD) 2. Non-sense protein 3. Selenoprotein formed. As alluded to by Larry, NMD is most likely to occur in most cases resulting in mRNA destruction, thus no protein is produced ...
written 6.2 years ago by Graslevy240

Latest awards to Graslevy

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Ethical Issues In Bioinformatics
Great Question 2.8 years ago, created a question with more than 5,000 views. For Bioinformatics Project Idea
Student 3.6 years ago, asked a question with at least 3 up-votes. For Ethical Issues In Bioinformatics
Appreciated 5.0 years ago, created a post with more than 5 votes. For Ethical Issues In Bioinformatics
Good Question 5.0 years ago, asked a question that was upvoted at least 5 times. For Ethical Issues In Bioinformatics
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Bioinformatics Project Idea
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Ethical Issues In Bioinformatics
Supporter 5.0 years ago, voted at least 25 times.
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How One Can Computationally Analyse The Functional Impact Of Frameshift Mutation
Student 5.0 years ago, asked a question with at least 3 up-votes. For Ethical Issues In Bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1302 users visited in the last hour