10X Genomics单细胞转录组测序数据的处理
Cellranger一步处理单细胞转录组测序数据 #!/bin/bash #Single Cell 3' v2 #R1----cell barcode and UMI 16+10bp --r1-length must >= 26 #R2----cDNA length #--expect-cells总是会遇到拿到的细胞数过少的问题，所以选用--force-cells强制规定细胞的数目 if [ $# -ne 7 ] then echo "Usage: ./cellranger.sh [id] [fastqpath] [sampleID] \ [cell_num] [t] [r1_length] [r2_length]" exit 65 fi id=$1 fastqpath=$2 sampleID=$3 cell_num=$4 t=$5 r1_length=$6 r2_length=$7 cellranger count --id=$id --fastqs=$fastqpath \ --transcriptome=/home/xxx/reference/refdata-cellranger-hg19-1.2.0 \ # download from cellranger website --sample=$sampleID --force-cells=$cell_num --localcores=$t --chemistry='SC3Pv2' \ --r1-length=$r1_length --r2-length=$r2_length