Intermediate files output by pipelines can be downloaded from the Pipeline tab
Overview
A BAM file (.bam) is the binary version of a SAM file (.sam), which is a tab-delimited text file that contains sequence alignment data. These formats are described on the SAM Tools web site: http://samtools.github.io/hts-specs/.
In Pluto, certain experiment pipelines (e.g. the automated nf-core/cutandrun CUT&RUN pipeline) output .bam files. These files can be downloaded for use in other scripts and programs.
Downloading BAM files in Pluto
On an experiment for which a pipeline was run, you can download BAM files from the Pipeline tab on the experiment page:
Don't see BAM files on your experiment?
Only experiments for which FASTQ files were uploaded and a pipeline was run will have BAM files, and not every experiment pipeline in Pluto will produce BAM files. Experiments created using a processed file format (e.g. CSV count matrix) will not have BAM files.
If you believe your experiment should have BAM files but you aren't seeing them in Pluto, feel free to reach out to our team using the chat bubble in the app and we'd be happy to help!