altanalyze question
Li, Haiqing
Hi! Altanalyze Development team,
I am try to following the rnaseq tutorial, but got lost at the step " Building a Dataset Exon Database for BEDTools(http://code.google.com/p/altanalyze/wiki/BAMtoBED)"
In the instructions - "At the bottom of this window, select the option "Build exon coordinate bed file to obtain BAM file exon counts". This will instruct AltAnalyze to select novel junction coordinates that correspond to novel exons to add to known Ensembl/UCSC exon regions."
But, in the last version 2.02, there is no "Build exon coordinate bed file to obtain BAM file exon counts" option.
What should I do for this step?
Thanks.
Best,
Haiqing
---------------------------------------------------------------------
SECURITY/CONFIDENTIALITY WARNING:
This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender.
---------------------------------------------------------------------
Nathan Salomonis
Right you are! Version 2.02 doesn't have this feature but version 2.03 does:
http://code.google.com/p/altanalyze/downloads/list
We have been testing this new version with different datasets and different analysis options to make sure everything is running smoothly before officially releasing it. Most of the documentation is also updated but we are also reviewing it as there are many new features added in this version and some bugs introduced, which should all be fixed now. If you want to try this candidate version, that is great, please just inform us of any issues or questions that arise.
Best,
Nathan
Li, Haiqing
Quick question for rnase analysis-if I only want to annotate the alt splicing event of a dataset, can I just use one junction data set? The default input of altanalyze are at least two dataset(one experment, one control).
Thanks!
Haiqing
________________________________________
From: Nathan Salomonis [nsalo...@gmail.com]
Sent: Tuesday, June 07, 2011 7:53 PM
To: Li, Haiqing
Cc: alt_pre...@googlegroups.com
Subject: Re: altanalyze question
Hi Li,
Right you are! Version 2.02 doesn't have this feature but version 2.03 does:
http://code.google.com/p/altanalyze/downloads/list
We have been testing this new version with different datasets and different analysis options to make sure everything is running smoothly before officially releasing it. Most of the documentation is also updated but we are also reviewing it as there are many new features added in this version and some bugs introduced, which should all be fixed now. If you want to try this candidate version, that is great, please just inform us of any issues or questions that arise.
Best,
Nathan
On Tue, Jun 7, 2011 at 7:20 PM, Li, Haiqing <ha...@coh.org<mailto:ha...@coh.org>> wrote:
Hi! Altanalyze Development team,
I am try to following the rnaseq tutorial, but got lost at the step " Building a Dataset Exon Database for BEDTools(http://code.google.com/p/altanalyze/wiki/BAMtoBED)"
In the instructions - "At the bottom of this window, select the option "Build exon coordinate bed file to obtain BAM file exon counts". This will instruct AltAnalyze<http://code.google.com/p/altanalyze/wiki/AltAnalyze> to select novel junction coordinates that correspond to novel exons to add to known Ensembl/UCSC exon regions."
But, in the last version 2.02, there is no "Build exon coordinate bed file to obtain BAM file exon counts" option.
What should I do for this step?
Thanks.
Best,
Haiqing
[cid:image0...@01CC2547.F6121E30]
Li, Haiqing
Thanks,
Haiqing
________________________________________
From: Li, Haiqing
Sent: Wednesday, June 08, 2011 1:44 AM
To: Nathan Salomonis
Cc: alt_pre...@googlegroups.com
Subject: RE: altanalyze question
Nathan Salomonis
Good question. Right now, this option doesn't exist but there are some
ways at getting at in AltAnalyze and other methods.
It seems like the best way to implement this would be to infer isoform
expression based on composite exon and junction expression, as is done
with TopHat, Scripture, MiSO, ERANGE and several other methods and
then look for pairwise isoform differences for any isoforms that
associate with a gene. Hence, I think these other methods are a good
starting point for doing these analyses, although, I feel that the
prediction methods will be problematic until we have a good method to
reliably quantify isoforms in the lab (e.g., full-transcript or
proteomic) for validation. Other issues are ensuring that each isoform
is a true transcript of that gene (shared single pre-mRNA) as opposed
to overlapping ncRNAs. We are interested in coupling some of these
methods with AltAnalyze and are currently investigating which
method(s) are most appropriate (best predictive power with the fewest
dependencies).
The isoform pairs associated by AltAnalyze are assigned with the
intention of finding transcript pairs which are most similar with
exception to the regulated exon region, or junction pairs. This allows
us to derive a conservative estimate of protein domain and motif-level
differences between transcript products.
Just looking at what AltAnalyze has now, you can open the file
"ExpressionInput/exp.YourDataset.txt" and see if competitive junctions
are expressed in a single sample. For example, if gene1:E10-E11 and
gene1:E10-E12 are expressed in a sample, then you have evidence of
alternative isoform expression within the sample. I recommend checking
out this data. Details on these junctions can be found in the file:
AltDatabase/EnsMart62/Hs/Ensembl_junction.txt in the same folder as
ExpressionInput.
Best,
Nathan
Nathan Salomonis
In a few output files from AltAnalyze, you will see the column
"probeset ID" when analyzing RNA-seq data. For example, in the
DomainGraph output file, you will see probeset ID as opposed to exon
or junction ID. For DomainGraph, this is truly an Affymetrix probeset
ID, specifically, the corresponding Affymetrix Exon 1.0 ST array
identifier that corresponds to a particular exon. Since DomainGraph
only works with Exon 1.0 array data right now, AltAnalyze grabs an
exon and looks up the Affymetrix probeset that overlaps with that exon
for DomainGraph, in order to visualize these results. These is
imperfect, as DomainGraph should ultimately view RNA-seq exon and
junction identifiers. This is something we plan to immediately work
on.
There may be other places that reference "probeset ID" for RNASeq
data. This is only because the same code processes both RNA-seq and
exon/junction array data (both boil down to sequence identifiers that
reference the same formatted database files). If you see this,
probeset ID refers to junction or exon ID from your RNA-seq
experiment. If the ID is of the type gene1:E1-E2 then it is a
junction. If it is of the type gene1:E1, it is an exon. If the ID
contains an underscore, e.g., gene1:E1-E2_1234567, the exon with the
underscore represents a novel junction splice site, inside exon E2
with the genome coordinate following the underscore.
Best,
Nathan
> --
> You received this message because you are subscribed to the Google Groups "Alternative Splicing and Functional Prediction" group.
> To post to this group, send email to alt_pre...@googlegroups.com.
> To unsubscribe from this group, send email to alt_predictio...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/alt_predictions?hl=en.
>
>