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Search: Posts Made By: JamieWizard
Forum: Bioinformatics 11-14-2017, 04:07 AM
Replies: 4
Views: 1,303
Posted By JamieWizard
Thanks JW. The reason I am asking is I'm...

Thanks JW. The reason I am asking is I'm interested in the biases introduced by different fragmentation methods. Enzymatic methods, such as restriction endonucleases are a different class.
...
Forum: Bioinformatics 11-13-2017, 10:37 AM
Replies: 4
Views: 1,303
Posted By JamieWizard
Cheers for that Torben. I saw that article, but...

Cheers for that Torben. I saw that article, but thought it looks like a masters and because it's not referenced elsewhere might therefore not be a standard method that is used in labs that do...
Forum: Bioinformatics 11-13-2017, 05:12 AM
Replies: 4
Views: 1,303
Posted By JamieWizard
Chemical shearing of DNA specifically (not RNA)

Hi,

I just wondered, are there any sequencing protocol kits around for shearing DNA by chemical means? I know that heating RNA in presence of divalent cations can be used to fragment RNA (i.e....
Forum: Bioinformatics 11-01-2017, 03:36 AM
Replies: 0
Views: 651
Posted By JamieWizard
Help!!! Non RNA-splicing/non poly-adenylation transcriptomics datasets

Hi all,

I am carrying out some transcriptomics analysis on RNA-seq data and wonder where I can find RNA-seq datasets (pre-aligned BAM/SAM files) for organisms which don't have RNA-splicing or...
Forum: General 05-13-2015, 01:12 AM
Replies: 0
Views: 818
Posted By JamieWizard
Poor metadata and experiment annotation in the SRA

Hi all,

Informing everyone of our recently published research paper: Investigation into the annotation of protocol sequencing steps in the sequence read archive
...
Forum: Bioinformatics 06-08-2014, 09:17 AM
Replies: 7
Views: 3,242
Posted By JamieWizard
SRA study numbers from 2013 - Bioconductor response

Hi everyone,

Thank you all for your thoughts. My initial thought based on another query was that a large proportion of the undated records could potentially be from 2013 (in light of the...
Forum: Bioinformatics 06-05-2014, 10:05 AM
Replies: 7
Views: 3,242
Posted By JamieWizard
SRA top level studies counts, why is 2013 so low?

Hi all,

I've been looking at the Sequence Read Archive (SRA) short read meta-data using the Bioconductor extracted SQLite data. (available from ...
Forum: General 10-07-2013, 09:16 AM
Replies: 0
Views: 890
Posted By JamieWizard
Zeus molecular visualisation software for Windows

Hi All,

Announcing Zeus, a powerful molecular visualisation tool supporting PDB/Brookhaven, MOL, MOL2/SYBYL and XYZ file formats. It incorporates a sophisticated rendering engine that can output...
Forum: General 10-07-2013, 08:29 AM
Replies: 3
Views: 1,856
Posted By JamieWizard
Zeus also allows users to label individual amino...

Zeus also allows users to label individual amino acids in a peptide/protein sequence. Amino acid residues are listed on the right hand side list, they can be labelled by selecting the tick under the...
Forum: Introductions 10-02-2013, 08:53 AM
Replies: 0
Views: 987
Posted By JamieWizard
Hello from the UK

Hi everyone,

I'm new to Bioinformatics and come from a Pharmacy/Chemistry and Software
Engineering background, I am currently looking into understanding Next Gen. Seq.
and RNA transcriptomics...
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