SAMMate 2.5

[xuguorong]

All-new SAMMate 2.5 is released.

http://sammate.sourceforge.net/

New features:
RAEM-Read Assignment via EM (Deng et al. 2011, Nucleic Acids Research, doi: 10.1093/nar/gkr042)
One-step iQuant (isoform Quantification, manuscript in preparation)
Iterative iQuant (isoform Quantification, manuscript in preparation)
Output read counts for detecting differentially expressed genes and differentially expressed transcripts. e.g. using edgeR

[questioner]

How long (approximately) does it take to quantify a transcriptome profiled with 15 million reads at isoform-level?

[tonge]

@ Xuguorong,
I haven't been able to find any information regarding small RNA deep sequencing and Sammate. Sammate looks very user friendly but I am wondering - Is sammate suitable for processing BAM files derived from a miRNA reads? and if so, what type of annotated track is best for visualising my miRNA data on sammate?
Thanks

[xuguorong]

Hi tonge,

The current functionalities are focused on mRNA isoform quantification and microRNA quantification would be released soon.

Thank you for using SAMMate!
Guorong