User: jrj.healey

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jrj.healey400
Reputation:
400
Status:
Trusted
Location:
United Kingdom
Website:
http://www2.warwick.ac...
Twitter:
JRJHealey
Last seen:
5 hours ago
Joined:
1 year, 5 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 • 129 results • page 1 of 13 • next >
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Comment: C: Extracting pairwise alignment info
... Ah yeah I see the problem. My approach probably isn't going to work overall then in that case. Sorry! ...
written 14 hours ago by jrj.healey400
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Comment: C: Extracting pairwise alignment info
... If you want the whole fraction (that was not what you asked for in your example output), you can modify my script to easily output the full fraction by removing the `%/*` parts in the last line. I've edited my answer to explain what it's doing as well. i.e.: echo -e "$name\t$length\t${percID% ...
written 15 hours ago by jrj.healey400
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Comment: C: Extracting pairwise alignment info
... `cut`, `grep`, `sed`, `awk`, `sort`, `uniq`, `cat`, `xargs`, `join`.. (and more besides).. all super useful for some quick and dirty chopping up of text :) ...
written 16 hours ago by jrj.healey400
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Answer: A: Extracting pairwise alignment info
... **EDIT** After more info from the OP, this solution doesn't work in all cases where the fractions digit lengths vary. ---------- This is neither pretty nor elegant, but it works. A more talented/persistent programmer will almost certainly be able to do it in one line without needing to recall `c ...
written 17 hours ago by jrj.healey400
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Comment: C: gnu parallel for RNA seq
... I have no idea what sort of timeframe it will take for each of your BAM files as you've not said how big they are. Are they still running after 8-9 hours or is that the finish time? Here's a little snippet of some code I used to sequentially ssh in to 11 VMs and start 30 protein structure simulatio ...
written 18 hours ago by jrj.healey400
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Comment: C: gnu parallel for RNA seq
... It's a bit confusing as to whether you're trying to simple process several files concurrently, or to (also?) call `cufflinks` to run in a multithreaded manner too? How big are your 4 (20?) files? Do you even really need to multithread them that badly? You could still invoke cufflinks 20 times, with ...
written 1 day ago by jrj.healey400
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Comment: C: gnu parallel for RNA seq
... just `ctrl-z` it to stop the job, then type `bg` to send it to the background (or just follow the command with an `&` in the first place). When you send `bg`, the job will resume, you can check whether it's running in `top`. Just because you aren't seeing any STDOUT doesn't mean it isn't runnin ...
written 1 day ago by jrj.healey400
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Comment: C: gnu parallel for RNA seq
... `cufflinks` has a `-p` option for utilising multiple threads, is that not what you're looking for? If you only have 4 samples, I would just run each one with a fourth of your total cores? e.g. `for file in ~/k/*/*.bam ; do cufflinks -p 13 -g gencode.v21.annotation.gtf -o WTL1 $file ; done` Or some ...
written 1 day ago by jrj.healey400
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Comment: C: Contamination in assembly
... Yeah we've since resolved it. It wasn't presenting an issue for our assemblies until we started working on aDNA samples and we're seeing suspect reads in Kraken. We now know that it can cause issues so are on the lookout for it. ...
written 3 days ago by jrj.healey400
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Comment: C: Contamination in assembly
... Ah ok, I've done it 'manually' in the past with `samtools` and `bwa` when I was trying to assemble plasmids from illumina data of lab strains. Only managed to get it to assemble into 1 perfect contig after discarding fragments of the host gDNA in the miniprep by alignment. Never actually used the `B ...
written 3 days ago by jrj.healey400

Latest awards to jrj.healey

Scholar 15 hours ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Centurion 17 days ago, created 100 posts.
Supporter 29 days ago, voted at least 25 times.
Scholar 4 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 4 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 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 6 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
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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