Does galaxy has "outFilterMultimapNmax" option in STAR and FeatureCounts ?

rna-star
#1

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 ?

#2

The option is available for STAR - just a bit hard to find (hidden under advanced advanced options :slight_smile: ):

  • Would you like to set output parameters (formatting and filtering)?: Yes
    • 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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#3

the score by default is 10, what should it be for mapping pseudogenes ?

#4

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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