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Forum: Bioinformatics 01-29-2014, 05:46 AM
Replies: 0
Views: 1,404
Posted By beans
Unhappy Assembly problems with fastx artefacts filter

Hi All,

I've been using the fastx toolkit to preprocess Illumina HiSeq reads for alignment using shrimp and assembly using Velvet/Oases. We've had some problems with using the artefacts filter:...
Forum: Bioinformatics 09-05-2012, 07:51 AM
Replies: 0
Views: 675
Posted By beans
Using an alternative aligner with MapSplice

Hello there,

I'm starting out using RNA-seq data to identify/ quantify alternative splicing in a variety of species. I'd like to use MapSplice as it seems quite flexible and performs well but I'd...
Forum: RNA Sequencing 11-03-2011, 09:45 AM
Replies: 6
Views: 3,228
Posted By beans
Hi, Sorry for the delayed response,I didn't...

Hi,

Sorry for the delayed response,I didn't realise there had been another reply to this. The replicates are simply different individuals that we wanted to sequence in order to get an idea of the...
Forum: RNA Sequencing 07-21-2011, 03:45 AM
Replies: 6
Views: 3,228
Posted By beans
Hi All, Thanks very much for your comments...

Hi All,

Thanks very much for your comments - I was hoping it would be fairly simply and that those packages would take replicates into account. It's difficult to anticipate these things first...
Forum: RNA Sequencing 07-19-2011, 07:34 AM
Replies: 6
Views: 3,228
Posted By beans
Differential expression from RNA-seq: variation between replicates

Hello,

Iím trying to figure out a method for analysing some RNA-seq data (and Iím very new to this so simple wording please!). I have 2 groups, each with 3 replicates. I want to:

1. assess...
Forum: Introductions 07-13-2011, 06:37 AM
Replies: 373
Views: 141,153
Posted By beans
Hello everyone, I'm a mature phd student,...

Hello everyone,

I'm a mature phd student, just dipping my toes into RNA-seq - I'm currently waiting for some wild samples that I collected on fieldwork to be sequenced so I'm reading up on...
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