BAM and BAM Index

Files:

[sample_name]_Bioproduct.bam
[sample_name]_Bioproduct.bam.bai
[sample_name]_ATAC.bam
[sample_name]_ATAC.bam.bai

Note:

  1. The *_Bioproduct.bam consists of reads arising from AbSeq, SampleTag, Targeted, VDJ or WTA assays.

  2. A Combined_ prefix is added to the bam and bai files when SampleTags are present in the experiment to signify that the resulting bam contains reads from all the samples.

BAM is an alignment file in binary format that is generated by the aligner and contains tags related to alignment quality. The Bioproduct BAM consists of alignments from the R2 reads only, whereas the ATAC BAM contains alignments from both the R1 and R2 reads. The BAM files are sorted according to the alignment coordinates of either the R2 read (Bioproduct) or both the R1 and R2 reads (ATAC) on each chromosome. The BAM Index is the index file associated with the coordinate-sorted BAM file.

The BD Rhapsody™ Sequence Analysis Pipeline further annotates the BAM files with the tags described below. For the Bioproduct BAM, if a read has multiple alignments (NH tag > 1), then only the first alignment (HI tag is 0 or 1) will be annotated along with all uniquely aligned reads. For the ATAC BAM, all reads will be annotated with the tags below.

TagDefinition
CBA number between 1 and 3843 representing a unique cell label sequence (CB = 0 when no cell label sequence is detected).
MRRaw molecular identifier sequence. (Bioproduct BAM only)
MARSEC-adjusted molecular identifier sequence. If not a true cell, the raw UMI is repeated in this tag. (Bioproduct BAM only)
CN

Indicates if a sequence is derived from a putative cell, as determined by the cell label filtering algorithm (T: putative cell; x: invalid cell label or noise cell).

Note: You can distinguish between an invalid cell label and a noise cell with the CB tag (invalid cell labels are 0).

STThe value is 1–24, indicating the Sample Tag of the called putative cell, or M for multiplet, or x for undetermined.
XFName of the Gene/AbSeq/SampleTag that a particular read was annotated to. (Bioproduct BAM only)

Note: A BAM file can be converted to a tab-delimited text file (SAM format) by using Samtools (see htslib.org)