I'm trying to get a regex to work with rename; I've tried the approach of similar answered questions here but couldn't get the results I wanted.

The files are named as such:

    SR1_S90_L001_R1_001.fastq.gz 
    SR1_S90_L001_R2_001.fastq.gz
    Rinc_S96_L001_R1_001.fastq.gz 
    Rinc_S96_L001_R2_001.fastq.gz

And I would like to retain only the information prior to the first underscore and the _R1_ or _R2_ tags, like this:

    SR1_R1_.fastq.gz
    SR1_R2_.fastq.gz
    Rinc_R1_.fastq.gz 
    Rinc_R2_.fastq.gz

Thanks in advance!
Try safe-batch-rename tool `brename` ( https://github.com/shenwei356/brename )

    brename -p '^(\w+?)_.+_(R[12])_.+' -r '${1}_$2.fq.gz'    # updated

    # original answer
    # brename -p '^(\w+)_.+_(R[12])_.+' -r '${1}_$2.fq.gz'
    # if you have ran this, you can run 'brename -u' to undo.


