Question: How do I input FASTQ files from resequenced libraries (sequenced across multiple lanes or flow cells) into the pipeline?
Answer: It is necessary to use the
--fastqs argument to specify the path(s) to the directory containing your FASTQ files. If you resequenced a single library (corresponding to a single channel on the Chromium chip) across two or more lanes or flow cells, for instance to increase depth of coverage, multiple values can be passed to the
--fastqs argument, separated by commas:
Additionally, there are three options that can further subset or combine the files within a given directory. The
--sample option is used to specify a subset of the samples in that directory based on the filename prefix. For example, you may have multiple files with different filename prefixes (sample1_1, sample1_2) that were demultiplexed separately that actually represent a single library:
You may also use the
--lanes option to subset based on lanes, and the
--indices option (only if you are analyzing older "demux" datasets). It is possible to pass multiple comma-separated values as above.
Important: Your FASTQ files must be named following the
bcl2fastq format (unless you are analyzing demux data):
Where Read Type is one of:
I1: Sample index read (optional)
R1: Read 1
R2: Read 2
For more information see Specifying FASTQs for 10x pipelines.