单细胞转录组分析---理解cellranger的输出的bam比对

1）bam文件

在outs文件中，有一个bam文件是根据我们的结果生成的：

这个文件有25+列，前面11列是标准的sam/bam文件输出，后面的列是cellranger文件生成的。

The cellranger pipeline outputs an indexed BAM file containing position-sorted reads aligned to the genome and transcriptome. Reads aligned to the transcriptome across exon junctions in the genome have a large gap in its CIGAR string i.e. 35M225N64M. Each read in this BAM file has Chromium cellular and molecular barcode information attached. Cell Ranger modifies MAPQ values; see the MM tag below. The following assumes basic familiarity with the BAM format. More details on the the SAM/BAM standard are available online.

所以根据官网的注释，我们可以看出各个列的意义如下：

所以：第10列是reads的序列文件，11列是reads的质量文件，CR是barcode ID，CY是barcode的测序质量，UR是UMI序列，UY是UMI测序质量。