User: jrj.healey

gravatar for jrj.healey
jrj.healey4.6k
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
Comment: C: GNU parallel error: Command line too long
... 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.healey4.6k
2
votes
2
answers
64
views
2
answers
Answer: A: Metatranscriptomics in sterile rooms
... 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.healey4.6k
0
votes
2
answers
70
views
2
answers
Answer: A: How to get plasmid or costruct sequence from fastq file in c.elegans Whole-genom
... 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.healey4.6k
0
votes
2
answers
70
views
2
answers
Comment: C: How to get plasmid or costruct sequence from fastq file in c.elegans Whole-genom
... 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.healey4.6k
0
votes
2
answers
162
views
2
answers
Comment: C: GNU parallel error: Command line too long
... 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.healey4.6k
0
votes
2
answers
162
views
2
answers
Comment: C: GNU parallel error: Command line too long
... 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.healey4.6k
0
votes
2
answers
52
views
2
answers
Comment: C: The fastest protein sequence aligner available
... +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.healey4.6k
0
votes
2
answers
52
views
2
answers
Comment: C: The fastest protein sequence aligner available
... 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.healey4.6k
0
votes
2
answers
162
views
2
answers
Comment: C: GNU parallel error: Command line too long
... 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.healey4.6k
0
votes
2
answers
162
views
2
answers
Comment: C: GNU parallel error: Command line too long
... 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.healey4.6k

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
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
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
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
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

Help
Access

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