User: Lythimus

gravatar for Lythimus
Lythimus200
Reputation:
200
Status:
Trusted
Location:
Last seen:
5 years, 7 months ago
Joined:
7 years, 3 months ago
Email:
j*****@uno.edu

Posts by Lythimus

<prev • 18 results • page 1 of 2 • next >
2
votes
20
answers
20k
views
20
answers
Answer: A: How To Organize A Pipeline Of Small Scripts Together?
... If you believe you are going to use your pipeline a fair amount over time I would recommend rake regardless of what language it's written in. If you believe other people would be interested in using your pipeline consider forking the Galaxy project and converting your scripts into modules for Galaxy ...
written 6.4 years ago by Lythimus200
0
votes
4
answers
3.8k
views
4
answers
Comment: C: Getting Number Of Reads In A Contig From Velvet Assembly
... Can this be done with ABySS as well? ...
written 6.6 years ago by Lythimus200
0
votes
3
answers
2.6k
views
3
answers
Comment: C: Quick Command To Split Large Blastx Files?
... Ketil, I was fairly sure I read they weren't comparable, but I may be wrong. I skimmed through where I thought I read it and couldn't find anything on it and didn't feel like doing the math/logic to see if they are, haha. ...
written 6.6 years ago by Lythimus200
0
votes
3
answers
2.6k
views
3
answers
Answer: A: Quick Command To Split Large Blastx Files?
... It depends on your output. BLASTXML can be parsed with something like the perl module XML::Merge, but this would consume a lot of memory and take a while, so I would recommend grabbing what is essentially the header and the footer of each file (the statistics at the end will be thrown off, but who c ...
written 6.6 years ago by Lythimus200
0
votes
8
answers
8.7k
views
8
answers
Comment: C: Huge Ngs Data Storage And Transferring
... Or you could just create UDP torrents. ...
written 6.6 years ago by Lythimus200
4
votes
4
answers
1.8k
views
4
answers
Answer: A: How To Change An Expertise In Bioinformatics
... See if you can get access to some NGS data (the link is dead at the moment) (EBI and NCBI should have plenty publicly available) and just familiarize yourself with NGS tools. Make sure you understand how the technology differs from say, microarrays, and read some of the more influential papers using ...
written 6.6 years ago by Lythimus200
2
votes
10
answers
3.6k
views
10
answers
Answer: A: What Kind Of Bioinformatics Tutorials Would You Like To See Online?
... I think Khader Shameer covered the spectrum fairly well. What I would like to see personally though is a primer on converting a command line-based pipeline into Galaxy. I'm becoming a fan of it but am personally having some issues with some of the advanced features and frankly can't find all the inf ...
written 6.6 years ago by Lythimus200
1
vote
2
answers
5.0k
views
2
answers
Answer: A: Analyzing Unknown Dna Sequence And Suggesting Origin
... I would recommend BLASTing against a compilation-based diverse database such as NT or WGS. You did well using an ORF finder, and I believe you should have a minimum gene cut off probably somewhere in the 200bp zone (don't forget to do reverse strand, overlaps are fine). If it is a eukaryote then the ...
written 6.6 years ago by Lythimus200
3
votes
1
answer
2.2k
views
5 follow
1
answer
Rna-Seq Contaminants Assembling Likelihood
... Assuming contaminants are introduced into my sample (some of my skin sloughs off or whatever) and I use RNA-Seq to sequence my samples, if I isolated those reads via taxonomical binning, what is the likelihood they would assemble using a de novo assembler such as ABySS or Velvet? Similarly, if read ...
assembly blast written 6.6 years ago by Lythimus200 • updated 6.6 years ago by Michael Dondrup43k
0
votes
3
answers
2.0k
views
3
answers
Answer: A: Full Exome Sequencing Of Xenografted Tumor
... I've been working on this problem and am searching for data sets such as yours to test it out on in which there is a known degree of contamination. Take a look and contact me if you are interested in pursuing: https://github.com/Lythimus/PARSES/ ...
written 6.6 years ago by Lythimus200

Latest awards to Lythimus

Supporter 5.7 years ago, voted at least 25 times.
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: How To Change An Expertise In Bioinformatics
Appreciated 6.7 years ago, created a post with more than 5 votes. For A: Where To Advertise Or Find Bioinformatics Jobs
Good Answer 6.7 years ago, created an answer that was upvoted at least 5 times. For A: Where To Advertise Or Find Bioinformatics Jobs
Teacher 6.7 years ago, created an answer with at least 3 up-votes. For A: Where To Advertise Or Find Bioinformatics Jobs
Popular Question 6.8 years ago, created a question with more than 1,000 views. For Ncbi Wgs/Nt/Env-Nt Databases

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1456 users visited in the last hour