STAR mapping output BAM files: Aligned.toTranscriptome.out.bam

Hi all,

When I mapped my RNAseq fastQ files using STAR in Galaxy, I got only one mapped.bam file. I was wondering if there is any way I could also get a Aligned.toTranscriptome.out.bam, which you would get from the STAR mapping using a command line platform.

Many thanks,

Hi Khanh,
the Galaxy tool version of STAR installed on the big public servers does not let you produce that file.
Their is an updated version available from the toolshed (so you could install it into your own instance of Galaxy right now), which supports this, but it will still take a bit of time before the new version makes it to public servers (the new version is based on STAR 2.7 so needs new genome indices built before people can really use it productively).

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That’s really helpful. Thank you, Wolfgang.