im working with pseudogenes and i think i need this option (outFilterMultimapNmax) but i cant find it in star or feature counts . does galaxy even has this option ?
The option is available for STAR - just a bit hard to find (hidden under advanced advanced options 
):
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Would you like to set output parameters (formatting and filtering)?: Yes
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Would you like to set additional output parameters (formatting and filtering)?: Yes
- Maximum number of alignments to output a read’s alignment results, plus 1
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Would you like to set additional output parameters (formatting and filtering)?: Yes
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the score by default is 10, what should it be for mapping pseudogenes ?
Please review this post at the STAR Google forum and see if it explains the usage you need:
https://groups.google.com/forum/#!topic/rna-star/gh5BFk1V2ko
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