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mshamblott started a topic Cufflinks settings on Galaxy

in Bioinformatics

05-18-2013, 03:40 PM
Cufflinks settings on Galaxy

I am trying to figure out the cufflinks run parameters. Here are the settings I have been using (basically default)

Max Intron Length:300000...

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hmortens started a topic modifying bowtie settings from tophat

in Bioinformatics

11-17-2011, 06:30 AM
modifying bowtie settings from tophat

*Hi,
I am attempting to modify the default settings that Tophat specifies for Bowtie to improve alignments.
I have tried the -g, -k, and...

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seqhorn started a topic Optimizing settings for mapping 100bp RNA-seq reads with tophat

in Bioinformatics

10-12-2011, 12:57 AM
Optimizing settings for mapping 100bp RNA-seq reads with tophat

Any ideas for optimizing tophat settings when mapping long reads (100bp RNA-seq single) to a reference genome?

So far we map around 30%...

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