Moderator: pld

gravatar for pld
pld4.7k
Reputation:
4,660
Status:
Trusted
Location:
United States
Last seen:
1 day, 6 hours ago
Joined:
5 years, 5 months ago
Email:
j*************@gmail.com

about me

Posts by pld

<prev • 661 results • page 1 of 67 • next >
1
vote
5
answers
609
views
5
answers
Comment: C: How to make bash script operate fast for a 13gb VCF.gz file with 900000 rows and
... At the very least just leave the file decompressed... ...
written 5 weeks ago by pld4.7k
0
votes
3
answers
194
views
3
answers
Comment: C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 3 months ago by pld4.7k
0
votes
3
answers
350
views
3
answers
Comment: C: Survey: help define Gencode and NCBI primary transcripts
... One thing to consider is that wet lab scientists come to these tools to find sequences for their uses. It's already hard enough to reconcile the gene name reported in a paper (e.g. Hsc70) with the myriad of things with that name (e.g. the 20 or so HSPA8s) before you get to the transcripts. For a w ...
written 4 months ago by pld4.7k
2
votes
1
answer
286
views
1
answers
Comment: C: Simplest output format of blast contamination check
... Try Kraken, its faster and can generate the kind of output you are asking for. ...
written 6 months ago by pld4.7k
0
votes
1
answer
498
views
1
answers
Comment: C: standalone blastp: increasing word size extremely slows down the search
... You may be able to save some overhead if you run BLAST directly from the command line, although not likely a meaningful amount. You may also try splitting the database up into multiple parts, just make sure you manually set the statistical options (e.g. dbsize). You'll have to do some post blast wor ...
written 12 months ago by pld4.7k
3
votes
2
answers
1.3k
views
2
answers
Comment: C: Is annotation of enhancers to nearest gene pointless?
... I think the paper says that 47% of elements impact the nearest TSS. The 7% is when considering looping interactions only. > Next we explored whether the relative order of elements in the genome > affects which long-range interactions occur. It is often assumed that > distal elements such ...
written 15 months ago by pld4.7k
0
votes
1
answer
884
views
1
answers
Comment: C: "Optimal" setting of CPU and max_memory in Trinity
... It is going to take a while, give it everything you've got. I wouldn't overthink this, you have a single small machine. I'd be more concerned about not having enough ram. ...
written 16 months ago by pld4.7k
1
vote
1
answer
668
views
1
answers
Comment: C: STAR command gets Killed
... HPC clusters all tend to have their own rules, features and etc. I have a feeling this might be a problem with how you're trying to run the job and not with STAR. Your cluster should have some kind of support team that should be better equipped to handle this issue. Assuming you're running Slurm, t ...
written 16 months ago by pld4.7k
0
votes
1
answer
516
views
1
answers
Comment: C: I want DATA SETS for Machine learning
... It even shows up on bing (near the bottom)! https://www.bing.com/search?q=mhc-1+binding+dataset&qs=n&form=QBLH&sp=-1&pq=mhc-1+binding+data&sc=0-18&sk=&cvid=D10100E784BF49CA8910BDB23DE298A4 ...
written 16 months ago by pld4.7k
0
votes
1
answer
516
views
1
answers
Comment: C: I want DATA SETS for Machine learning
... First hit when you google "mhc-1 binding dataset". The third hit is even from an AI lab: http://ailab.ist.psu.edu/red/mhci.html ...
written 16 months ago by pld4.7k

Latest awards to pld

Popular Question 4 days ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Popular Question 17 days ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 28 days ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 3 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 3 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 4 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 4 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 4 months ago, created a question with more than 1,000 views. For Assemble PCR Product Sanger Sequences
Popular Question 4 months ago, created a question with more than 1,000 views. For Generate a VCF File for Different Reference Sequences
Popular Question 5 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 5 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 6 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 6 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 6 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 9 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Popular Question 9 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Popular Question 10 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 11 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 12 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 13 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 13 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 13 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 460 users visited in the last hour