User: jrj.healey

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jrj.healey810
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Location:
United Kingdom
Website:
http://www2.warwick.ac...
Twitter:
JRJHealey
Last seen:
6 seconds ago
Joined:
1 year, 6 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 • 207 results • page 1 of 21 • next >
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Comment: C: MutScan: detect and visualize target mutations by just scanning FastQ, 50X faste
... Possible stupid question - your Github/post mentions cancer mutations specifically (as an example) - is this software generally applicable? e.g. bacterial resistance mutation detection? ...
written 44 minutes ago by jrj.healey810
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... I seem to remember MATLAB having the ability to convert/export in to compilable C code (not sure what flavour)? Perhaps you could just export, then you can release the C code as open source. But yeah, a MATLAB academic subscription is several thousand £/$ so you'll struggle with usership if left as- ...
written 59 minutes ago by jrj.healey810
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Answer: A: GC percent detection for several number of genes
... Partial solution for you. I don't know offhand how you can go about getting sequences for all your gene identifiers (I'm sure there's a way through NCBI though), but here's a script that'll calculate GC content (among other things) once you have all the nucleotide fastas: #!/usr/bin/python ...
written 20 hours ago by jrj.healey810
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Answer: A: Protein selection from BLASTp result.
... I'm not sure what the question is exactly, but it sounds like you're asking what the best result is? Your best match from BLAST will have an E-Value as close to 0 as possible (0 is as good as it gets), and ideally will have a large Bitscore. You may need to look at the query coverage etc however if ...
written 22 hours ago by jrj.healey810
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Comment: C: installing an R package
... Sounds like your version of R is out of date (which it is, we're up to 3.3.3 now I believe) ...
written 1 day ago by jrj.healey810
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Comment: C: Assembling a genome
... SPAdes doesn't take a reference as its a *de novo* assembler, though you could provide a file of trusted contigs if you wanted to. You might however want to check read quality and coverage in which case you may well need a reference genome. As for "how" you choose it, you simply download the genome ...
written 2 days ago by jrj.healey810
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Comment: C: defining consistent plot areas in ggtree
... Does this work for an individual tree? I'm not sure if I made it unclear in the OP, I'm passing in a single tree at a time from the commandline. Adding `+ facet_wrap(~.id)` to the first `ggtree(tree.obj)` line gives me the following error: `Error in combine_vars(data, params$plot_env, vars, drop = ...
written 4 days ago by jrj.healey810
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defining consistent plot areas in ggtree
... I'm trying to put together a script that I hope will be able to do general purpose graphical plotting of newick trees, using `ggtree`, since I like the graphics it produces - but I'm having a real battle with the scaling. All the trees represent RAxML created phylogenies of various orthologous genes ...
R ggtree written 4 days ago by jrj.healey810
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Answer: A: Cloning software design
... SerialCloner (Not sure if free) SnapGene Viewer A Plasmid Editor ("ApE") ...are all ones I use regularly (though the full paid version of SnapGene is my favourite so far) ...
written 5 days ago by jrj.healey810
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Answer: A: Local blast custom databases
... Do you have reference genomes for your bug and/or probable contaminants? You can simply map and discard/keep reads accordingly with the `-F` flag of `samtools`, before assembling. I've done this to remove host DNA from plasmid purifications in order to assemble the plasmids properly. Have you trie ...
written 5 days ago by jrj.healey810

Latest awards to jrj.healey

Scholar 21 hours ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 5 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
Scholar 16 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 17 days ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Scholar 17 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 17 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
Scholar 23 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 23 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 27 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
Scholar 27 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Centurion 7 weeks ago, created 100 posts.
Supporter 9 weeks ago, voted at least 25 times.
Scholar 9 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 9 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 11 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 11 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
Autobiographer 11 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 11 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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