User: jrj.healey
jrj.healey • 4.6k
- Reputation:
- 4,600
- Status:
- Trusted
- Location:
- United Kingdom
- Website:
- http://www2.warwick.ac...
- Twitter:
- JRJHealey
- Last seen:
- 34 minutes ago
- Joined:
- 2 years, 9 months ago
- Email:
- j*********@gmail.com
PhD Student at the Molecular Organisation and Assembly in Cells Doctoral Training Centre, University of Warwick.
PhD is lab based primarily, utilising synthetic biology for drug delivery applications, but something of an amateur enthusiast when it comes to bioinformatics/programming. Trying to absorb as much as I can.
Decent amount of experience with molecular simulation, genomics (including assembly, QC, annotation, comparative genomics), transcriptomics, proteomics, phylogenetics etc.
Posts by jrj.healey
<prev
• 942 results •
page 1 of 95 •
next >
0
votes
2
answers
162
views
2
answers
... Perhaps you're right, but I think my point still stands. I think to expect a significant change in how `parallel` handles CLI args is wishful thinking (especially for something that is a little bit of an edge case), so you'd be better off coming up with a robust way to get around this. There are loa ...
written 2 hours ago by
jrj.healey • 4.6k
2
votes
2
answers
64
views
2
answers
... You may want to take a look at the Ancient DNA field. They've developed many protocols and approaches recently to deal with low abundance of DNA, and DNA which is highly degraded.
It's been picking up a lot of steam in the last ~5 years or so in particular so you should find some recent papers.
AF ...
written 3 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
70
views
2
answers
... Here's an approach which might work:
1. Align all your reads in your fastq to your known plasmid sequence (you might need to experiment with some stringency).
2. *de novo* assemble your remaining reads to see if you regenerate the complete plasmid sequence.
3. Hopefully, the reads which span th ...
written 3 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
70
views
2
answers
... You are unlikely to find a tool 'ready made' for this. You're going to have to get your hands dirty. ...
written 4 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
162
views
2
answers
... Yeah so your problem is not with `parallel`, it's with the Unix cli limit, so you need to be a little cleverer about how you're doing it.
Besides, concatenating 10,000 files single line files, is the same as concatenating 10 x 1000 line files.
I would use `find` to build up the list and do the con ...
written 5 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
162
views
2
answers
... Why not `cat` all the files beforehand, and pass the file either directly to MAFFT, or via STDIN (if you have your heart set on piping)?
A workaround for `cat`ing more files than the commandline can handle would be to build up a list of the files using `find` and then `-exec`, then simply tell it t ...
written 6 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
52
views
2
answers
... +1 for pretty much all the above suggestions. Muscle in particular is crazy fast.
Clustal Omega gives some of the most accurate protein alignments to my knowledge, even if its a little slower, so it depends what you're trying to do/show. ...
written 6 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
52
views
2
answers
... It is a local aligner, but that is very different from doing, for example, a multiple sequence alignment (even if the MSA does local alignment). ...
written 6 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
162
views
2
answers
... Can you chunk your file list using `split` or similar? Or is it required for all of the arguments to be in that command? ...
written 6 hours ago by
jrj.healey • 4.6k
0
votes
2
answers
162
views
2
answers
... Is the command itself too large, or is it the list of arguments/files that you're passing to it that is exceeding the limit? ...
written 8 hours ago by
jrj.healey • 4.6k
Latest awards to jrj.healey
Scholar
1 day ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Appreciated
8 days ago,
created a post with more than 5 votes.
For A: Replace Sequence IDs in many text files (newick format) - Change script
Scholar
14 days ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Appreciated
5 weeks ago,
created a post with more than 5 votes.
For A: Replace Sequence IDs in many text files (newick format) - Change script
Good Answer
5 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Should I quit PhD program?
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar
3 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar
3 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Scholar
3 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Merging gff/gbk to create a 'full' gbk
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Scholar
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Scholar
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar
6 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1939 users visited in the last hour