10x Genomics data are stored in three FASTQ files, besides the standard R1 and R2 reads, there is also a I1 file with some metadata. Sometimes however they are shipped in a single bam/cram file (e.g. the data from the Darwin Tree of Life). How can I convert the BAM or CRAM files to FASTQ?
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Apparently, the I3 file is not 10x specific thing. It is an index generated when demultiplexing any Illumina data. See this question for a nice explanation.