User: i.sudbery

gravatar for i.sudbery
i.sudbery990
Reputation:
990
Status:
Trusted
Location:
Sheffield, UK
Twitter:
IanSudbery
Last seen:
12 hours ago
Joined:
1 year, 11 months ago
Email:
i********@sheffield.ac.uk

Posts by i.sudbery

<prev • 113 results • page 1 of 12 • next >
0
votes
3
answers
202
views
3
answers
Comment: C: Opinion: Bioinformatician - What comes first? Biology vs Informatics.
... The corollary to this is that if you are a informatician first, you'll struggle not to spend all your time answering other peoples requests rather than guiding your own work. ...
written 12 days ago by i.sudbery990
0
votes
1
answer
166
views
1
answers
Comment: C: Normalisation of arrays with global changes expected
... We are looking at RNA processing genes, so there is no reason to suspect that "housekeeping" genes wouldn't also be affected, but I'll look into the rank invariance thing. ...
written 16 days ago by i.sudbery990
0
votes
1
answer
166
views
1
answers
Comment: C: Normalisation of arrays with global changes expected
... Its human 293 cells. The data are single channel, so no dye swaps i'm afraid. ...
written 16 days ago by i.sudbery990
1
vote
1
answer
166
views
1
answer
Normalisation of arrays with global changes expected
... I've picked up an analysis that has been sitting in someone's drawer for a while. Its an Agilent array experiment where global changes are expected between the control and the treatment. The person who originally did the analysis (on GeneSpring :( ) stated in their material and methods that they use ...
microarray normalisation limma written 16 days ago by i.sudbery990 • updated 16 days ago by patrick.bradley30
0
votes
2
answers
190
views
2
answers
Comment: C: The right pipline with cufflinks, cuffmerge and cuffdiff
... Yeah, I'm pretty sure the input requirements are the same as cufflinks. ...
written 17 days ago by i.sudbery990
0
votes
1
answer
176
views
1
answers
Comment: C: settings optional parameters bwa mem
... If you plan to use the GATK pipeline downstream, I think you will need to use the -M option to BWA-MEM to make the BAMs it outputs compatible with Picard. ...
written 17 days ago by i.sudbery990
1
vote
2
answers
190
views
2
answers
Comment: C: The right pipline with cufflinks, cuffmerge and cuffdiff
... StringTie does almost exactly the same thing as cufflinks. We have found it a) to assemble few false positive transcripts b) Be an order of magnitude quicker and have a lower memory footprint than cufflinks. ...
written 17 days ago by i.sudbery990
2
votes
2
answers
226
views
2
answers
Answer: A: Gene list overlap - Null distribution
... As was mentioned by @Lars Juhl Jensen, the standard null distribution for two gene lists is the hypergeometric distribution. However, this assumes that all genes are independent and equally likely to show up. There are several reasons why this might not be the case: * Longer genes are more likely ...
written 5 weeks ago by i.sudbery990
0
votes
2
answers
209
views
2
answers
Comment: C: Publicly available RNA-seq data of neurons from human
... GTEx has brain data, but not specifically neuron data. ...
written 5 weeks ago by i.sudbery990
0
votes
2
answers
159
views
2
answers
Comment: C: mapping read is low for miRNA data after trimming
... Its been a while since I last did miRNA analysis, but when I did, the size distribution was pretty tight around 22nt. Maybe we didn't use the Illumina prep. This was the size distribution on the last analysis I did. ![][1] In fact, I highly recommend the [SequenceImp][2] miRNA precessing pipeline. ...
written 5 weeks ago by i.sudbery990

Latest awards to i.sudbery

Centurion 6 weeks ago, created 100 posts.
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 4 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
Scholar 5 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Scholar 6 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Alternative to Cufflinks ?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 6 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 6 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 870 users visited in the last hour