User: i.sudbery

gravatar for i.sudbery
i.sudbery2.4k
Reputation:
2,380
Status:
Trusted
Location:
Sheffield, UK
Twitter:
IanSudbery
Last seen:
12 hours ago
Joined:
3 years, 4 months ago
Email:
i********@sheffield.ac.uk

Posts by i.sudbery

<prev • 220 results • page 1 of 22 • next >
1
vote
3
answers
136
views
3
answers
Comment: C: RNASeq DGE : Kallisto-sleuth Vs Ballgown
... I've not really used the ballgown pipeline beyond playing about with it. My own preferred pipeline is `salmon` -> `tximport` -> `DESeq2`, although I can see the conceptual advantages in using `sleuth`. If I want an experiment specific transcript annotaiton, I'll assemble that first with string ...
written 2 days ago by i.sudbery2.4k
2
votes
3
answers
136
views
3
answers
Answer: A: RNASeq DGE : Kallisto-sleuth Vs Ballgown
... There are two main differences between the Kallisto-sleuth pipeline and the 'Ballgown' pipeline. Sleuth makes use of Kallisto's bootstrap analyses in order to decompose variance into variance associated with between sample differences and variance associated with quantificaiton uncertainty. I don't ...
written 7 days ago by i.sudbery2.4k
1
vote
8
answers
299
views
8
answers
Answer: A: Should bioinformaticians learn the scientific names of plants and animals?
... To add to what others have said, knowing a lot of these is probably not useful, but being able to *recognise* the common ones will probably be helpful (know what they are when you see them, but neccesarily be able to write them yourself). I doubt anyone "learnt" these deliberately, they just become ...
written 9 days ago by i.sudbery2.4k
0
votes
0
answers
70
views
0
answers
Comment: C: What files should I ask for from protein array analysis, in order to carry out d
... I don't know about file formats for protein arrays, but my guess is that the data is going to be similar in format to microarray data: a large number of florescence intensity readings in a spatially arrayed format. Thus you will probably be able to analyse the data with limma, although it will proba ...
written 16 days ago by i.sudbery2.4k
1
vote
5
answers
1.1k
views
5
answers
Answer: A: SRA to fastq
... Not quite an answer to the question you are asking, but the ENA (European Nucleotide Archive) has all publically available SRA samples for download directly as fastq. The download will take much longer (unless you use aspera), but the you more than make up for it in conversion time. ...
written 16 days ago by i.sudbery2.4k
1
vote
1
answer
113
views
1
answers
Comment: C: What is the recent preference for RNA-seq read deposition perior to publication
... I always deposit in GEO (which automatically forwards to SRA/ENA). I've never had any stress with it. Its dull, yes (copying the same info across many boxes), but I can't say a dataset has ever taken me more than a few hours. ...
written 4 weeks ago by i.sudbery2.4k
3
votes
1
answer
113
views
1
answers
Answer: A: What is the recent preference for RNA-seq read deposition perior to publication
... GEO (US) or ArrayExpress (Europe), depending on preference. It doesn't really matter which because if you deposit in one, it will be automatically mirrored in the other. Also submission to either results in automatic submission of your data to SRA / ENA. FAIRsharing is a database of databases, it ...
written 4 weeks ago by i.sudbery2.4k
0
votes
1
answer
176
views
1
answers
Answer: A: GOseq Probability Weight Function Interpretation and Use
... I think your problem is probably in this line here: lengthData=median(width(txsByGene)) What you are doing here is getting the length of the primary transcript: i.e. the distance from the TSS to the TTS. Actually what you need is the sum of the exon lengths (i.e. excluding the introns). You ca ...
written 5 weeks ago by i.sudbery2.4k
2
votes
1
answer
120
views
1
answers
Answer: A: how can I get long non coding RNA from RNA-seq data
... There are many reviews on this subject of find lncRNAs. Try this [one][1] and this [one][2] for starters. Both of these concentrate on species where the genome is available, but have some useful tips if you are looking to put together a protocol for doing in an unannotated genome. I guess you' ...
written 5 weeks ago by i.sudbery2.4k
1
vote
2
answers
119
views
2
answers
Answer: A: Best database for human mRNA expression information from different tissues?
... I personally like EBI's [Expression Atlas][1],but I don't think the eye is one of their tissues. In fact I'm not aware of any expression atlas that includes the eye (not saying it doesn't exist). [1]: https://www.ebi.ac.uk/gxa/home ...
written 5 weeks ago by i.sudbery2.4k

Latest awards to i.sudbery

Appreciated 29 days ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: if I am right about miRNA DE workflow
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
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?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 3 months ago, created a post with more than 5 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?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 8 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 9 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Scholar 10 months ago, created an answer that has been accepted. For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Alternative to Cufflinks ?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering during RNA Seq analysis?
Supporter 11 months ago, voted at least 25 times.
Appreciated 11 months ago, created a post with more than 5 votes. For A: Alternative to Cufflinks ?
Scholar 13 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: 1052 users visited in the last hour