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。
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