Re: [galaxy-user] Cuffdiff no without replicates

[Sean Davis]

On Wed, Oct 3, 2012 at 7:35 AM, Ross ross.laza...@gmail.com wrote:
 On Wed, Oct 3, 2012 at 9:11 PM, i b ibse...@gmail.com wrote:
 Dear all,
 how reliable is running Cuffdiff without replicates? e.g.one samples
 agains another one?

 Is it statistically makign any difference when using replicates?

 Seqanswers might be a better place to ask this very interesting
 technical question that goes way beyond Galaxy...

 My 2c: Statistically speaking, sequencing and biology are both noisy.
 Replicates provide information about non-experimental (technical and
 biological) variation. That variation is usually not the variation you
 are looking for, but if you want to remove it, you have to model it
 and that requires information from replicates (or really good
 guesswork). In some situations (eg extreme experimental conditions),
 I'm sure you'll find biologically meaningful signal without them but
 in my experience, they can really help to decrease non-experimental
 noise, particularly where the experimental condition induces only
 subtle changes in transcript abundance.

 You could always analyse a data set with replicates and compare the
 results with and without those replicates yourself to see what happens
 - it would be a nice paper I'm sure.

A bit off-topic, but you might take a look here:

http://www.ncbi.nlm.nih.gov/pubmed/21747377

In short, one needs replication in biology, regardless of the
technology used.  In particular, one would never suggest running a
microarray experiment without replicates; one should follow
approximately the same rules for sequencing (and sequence data
analysis).

Sean


 Thanks,
 ib
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:

   http://lists.bx.psu.edu/
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] How to decide Mean Inner Distance between Mate Pairs?

[Sean Davis]

On Wed, Aug 15, 2012 at 11:13 AM, Du, Jianguang jia...@iupui.edu wrote:

  Dear All,

 I am analyzing the downloaded RNA-seq datasets. However I am not sure how
 much is Mean Inner Distance between Mate Pairs for these paired-end
 datasets.

 Take a paired-end RNA-seq dataset as an example, there is a description
 for this dataset in SRA database of NCBI: Layout: PAIRED*, Orientation: *
 5'-3'-3'-5'*, Nominal length: *400*, Nominal Std Dev: *20

 At first I thought the Mean Inner Distance between Mate Pairs should be
 325bps because the length of reads on both ends is 36bps. However
 when I aligned the sequence of the paired reads on to transcripts and
 genome using BLASTn, the distance between the paired reads is about 200bps.
 How should I decide the Mean Inner Distance between Mate Pairs in my case?


The information from SRA is likely only an approximation.  SRA does not
validate these details, I do not think.

You can probably use the distribution from your data as the best estimate.

Sean

Thanks.

 Jianguang Du

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/