Hello James,

For coverage, a rough coverage attribute is available in the Cufflinks' GTF file. Absolute coverage is not calculated because RNA-seq reads can map to multiple isoforms and it's not possible to say which one it truly maps to (hence the need for Cufflinks' statistical models).


To address some of the other statistics, the tool "NGS: SAM Tools -> flagstat" provides some basic counts for BAM files.

For the rest, you will need to use a combination of the tools available for file conversions and data manipulation found in tool groups such as "Text Manipulation", "Filter and Sort", "Join, Subtract and Group", and the "NGS*" groups.

As an example, to identify the reads mapping to particular elements: convert Tophat's mapped reads to intervals (BAM-to-SAM, then SAM-to-interval) and intersect those coordinates with subsets of a GFF file (created using GFF filtering by keyword, e.g. "exon"). Then use the Group tool to generate counts.

Most sorts of manipulations one would do with simple scripting to gather counts are possible. Once you work out how to generate a particular statistic, be sure to save the steps into a workflow for future use (and consider publishing it for others to use).

Hopefully this helps!

Best,

Jen
Galaxy team

On 7/6/11 1:16 PM, James Chitwood wrote:
Hi all,
Is there any way to find out the number of reads aligning to a
transcript rather than the FPKM calculated by Cufflinks?

I'm also interested in obtaining summary statistics for mapping analyses
or RNA-Seq data, such as % of  reads aligned, % uniquely aligned, mapped
to exons, introns, etc.  Is there a tool that would provide a summary
table with this information?

Thanks for your help and providing this great resource,
James



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