sRNA single-sample mode alignment output

[malloryfreeberg]

Hi! I've run the single-sample mode for 6 small RNA-seq libraries (triplicates in two conditions), and I want to do some downstream analyses outside of piPipes based on the quantification of small RNAs against various features (e.g. transposons, piRNA clusters). The workflow diagram at the bottom of the small RNA-seq page shows that the transcriptome mapping step done by bowtie produces SAM/BAM formatted output files, and that an abundance estimation step is performed with eXpress against transcripts, transposons, and piRNA clusters. I am interested in using both the bowtie SAM/BAM output files and the eXpress output files for further analysis, but I can't seem to find them in the directory produced by running piPipes. Can you tell me where these files might be located? Or whether I need to include a particular option in the piPipes call to obtain these output files? Thank you!