Example BAM file for sciCSR analysis

BAM file corresponding to the BCP004_Total library from E-MTAB-9005 on ArrayExpress. Paper: https://doi.org/10.1126/sciimmunol.abe6291 ArrayExpress link: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-9005 The relevant samples FASTQ files were downloaded (H2FWCBGXB_BCP004_Total,H2MJFBGXB_BCP004_Total,HFH5VBGX7_BCP004_Total,HHLVCBGX9_BCP004_Total,HNGLMBGX7_BCP004_Total,HWHFLBGX9_BCP004_Total,HWNM7BGX5_BCP004_Total) and the following command for 'cellranger count' was run to perform sequence alignment. ``` $HOME/cellranger-3.1.0/cellranger-cs/3.1.0/bin/count --id=BCP004_Total --sample=H2FWCBGXB_BCP004_Total,H2MJFBGXB_BCP004_Total,HFH5VBGX7_BCP004_Total,HHLVCBGX9_BCP004_Total,HNGLMBGX7_BCP004_Total,HWHFLBGX9_BCP004_Total,HWNM7BGX5_BCP004_Total --chemistry=fiveprime --transcriptome=./refdata-cellranger-GRCh38-3.0.0 --fastqs=./ ```