If you set outSAMattributes as All then the sam file generated is incompatible with Cufflinks. The error is something like no XS tag for a spliced read. But when one uses outSAMattributes in standard mode and pass the sam file to cufflinks then no error is thrown. i think too many new tags when using the All mode create confusion for Cufflinks.

Also, i would appreciate if you could add a command line option to add RG, LB, SM, PL tags in the SAM file.

What version of the product are you using? On what operating system? Latest released version 2.3.0.1 on Linux

Please provide any additional information below.

when you specify --outSAMattributes All option, STAR outputs extra attributes that follow some novel SAM specifications. These attributes are only supported by the latest versions of samtools, 0.1.18 and 0.1.19, and will also cause problems with some downstream analysis software such as bedTools, HTseq and Cufflinks, because, I believe, these software do not use the latest samtools API.

I do not recommend using this option unless you really need these attributes. You can also cut the columns with these attributes before feeding the alignments to other software.

I will add the @RG tags in the next STAR release.

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