Moderator: jrj.healey

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jrj.healey6.1k
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http://www2.warwick.ac...
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JRJHealey
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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 • 1,181 results • page 1 of 119 • next >
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Comment: C: BLAST based on 100k sequences rnaseq?
... An artifical assignment was what I meant. What you are talking about is a different issue though.. If it doesn't exist in nr/nt, then why would you ever suppose BLAST would work in the first place? If its a novel organism, the best you can do is try to place it phylogenetically. You could in princ ...
written 11 hours ago by jrj.healey6.1k
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Comment: C: BLAST based on 100k sequences rnaseq?
... If this is a homework/assignment question you should be transparent about that in the opening post. If that is the case, I doubt they’ve have given you mixed data, in which case follow genomax’s suggestion of just blasting a handful of reads and any one of them will likely reveal the original organ ...
written 15 hours ago by jrj.healey6.1k
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Comment: C: BLAST based on 100k sequences rnaseq?
... I'd agree with using a tool like Kraken/Centrifuge. Blasting that many sequences will take a long time (I've done it), and the data that comes back is so enormous is almost impossible to do anything with it. I once BLASTed a set of sequencing reads to figure out what was in it, even with some very s ...
written 16 hours ago by jrj.healey6.1k
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Comment: C: Comparing reads of multiple BAM files (using getopts for parsing)
... `ls` provides no protection against malformed filenames, special characters etc. There are countless stackoverflow rants about this exact topic: https://unix.stackexchange.com/questions/128985/why-not-parse-ls https://mywiki.wooledge.org/ParsingLs Even if you didn’t want to use find, you can stil ...
written 18 hours ago by jrj.healey6.1k
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Comment: C: Comparing reads of multiple BAM files (using getopts for parsing)
... Would be better to do `for i in $(find ...)` - it’s considered bad practice to parse the output of `ls`. ...
written 18 hours ago by jrj.healey6.1k
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Comment: C: Batch pairwise alignment and consensus
... The consensus of a pairwise alignment isn’t possible/meaningful... how can you choose between one base or the other? Or are you just after all the sites which are identical? Can you please elaborate the purpose? ...
written 19 hours ago by jrj.healey6.1k
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Answer: A: Comparing reads of multiple BAM files (using getopts for parsing)
... I’m tempted to close this as it’s really just a programming question, unless you can rephrase it somehow, but I got started with the answer so here it is: —————— Your `getopt` looks fine. You just need to use the variables assigned in the `case` switch downstream. What you will need to do however ...
written 19 hours ago by jrj.healey6.1k
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Comment: C: samtools error #E27
... No Ram simply pointed out that you had used the wrong post type (this Is a question not a tool). The existing question is in the right place (there isn’t anywhere else). This error is documented though, and points to improper installation it seems. https://groups.google.com/forum/m/#!topic/jaffa-p ...
written 23 hours ago by jrj.healey6.1k
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Comment: C: How to access the score of a parsimony tree using biopython
... 1. In principle I would assume that’s possible. Whether it is easily done within Biopython is another matter. I don’t personally know (and am not currently at a computer to experiment), but if you could get intimate with the Phylo package source, you might be able to find something you can hook in t ...
written 23 hours ago by jrj.healey6.1k
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Comment: C: Blast With Biopython
... Please use the code formatting button (it has`101010` written on it in the bar above) to improve your posts readability. ...
written 23 hours ago by jrj.healey6.1k

Latest awards to jrj.healey

Appreciated 9 hours ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Teacher 11 hours 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 1 day ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 2 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
Teacher 6 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 6 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 13 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 14 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For C: Exporting sequences from Excel
Scholar 20 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 20 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 20 days ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Teacher 20 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 20 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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
Oracle 4 weeks ago, created more than 1,000 posts (questions + answers + comments).
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
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For C: Exporting sequences from Excel
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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 7 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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