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altanalyze
Alternative splicing and functional prediction analysis tool
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FAQ
Frequently Asked Questions
Featured
Updated
Oct 9, 2011
by
nsalomo...@gmail.com
AltAnalyze
Frequently Asked Questions
Main Analysis Options
What operating systems is AltAnalyze compatible with?
Can I run AltAnalyze on a remote machine without using the graphical user interface?
How can I visualize splicing and domain level changes from AltAnalyze?
What microarrays can AltAnalyze work with?
Can AltAnalyze work with exon/junction data for an unsupported platform (e.g., custom array)?
What is the difference between the splicing-index, FIRMA, MiDAS, Linear Regression and ASPIRE methods?
How can I annotate my splicing results from another program in AltAnalyze?
Installing
AltAnalyze
Why Does AltAnalyze crash when trying to download the database when first run?
Data Analysis and Import
What files do I need when analyzing Affymetrix arrays?
When I have dozens of samples in my study, how can I more easily assign the samples to groups than one by one?
What is the recommended cutoff for expressed genes with RNA-Seq?
Why does AltAnalyze need to filter my data?
Should I calculate gene expression using constitutive or all mRNA aligning probests?
How does a pair-wise alternative exon analysis differ from multiple group comparisons?
Why do I need to define groups and comparisons?
Why doesn't AltAnalyze run GO-Elite by default?
Why does AltAnalyze download the Gene 1.0 transcript annotation file for Exon 1.0 array analyses?
How can I remove probesets with sequence that aligns to multiple genomic loci from my analysis?
Can AltAnalyze return transcript cluster results instead of Ensembl for the Gene 1.0 array?
Probeset Alignments and
DomainGraph
How do AltAnalyze probeset-to-gene and probeset-to-exon mappings differ from those in the Affymetrix annotation files?
In AltAnalyze a probeset associated with an intron is predicted to alter protein domain composition of the protein, but in DomainGraph why don't I see the probeset?
How do I start DomainGraph and what can I do in DomainGraph?
Interpreting Alternative Exon Results
Why don't the folds and expression values from my RNA-seq experiment don't seem to match correctly?
What is a constitutive exon/junction?
Which results should I validate?
If two probesets align to one exon and have opposite splicing changes, what does this mean?
What does the (+) and (-) mean proceeding a protein domain, miRNA binding site or protein identifier?
What does the identifier E2-3 indicate and where does this annotation come from?
Where do the alternative splicing annotations provided in the column "exon annotations" come from?
What does the column "distal exon-region-ID" indicate?
What is the adjusted fold versus the non-adjusted fold change?
Why do all alternative exons have the indicator "exon-inclusion" in the column "event_call"?
How can I graph my splicing scores for all exons in a gene?
What is the difference between exon-level and gene-level alternative exon results?
When viewing AltAnalyze results in DomainGraph, why don't the identifiers match to my array/RNA-seq platform?
Other
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