# Step 1: Identify correct cell barcodes umi_tools whitelist --stdin CRISPR_STD_CKDL230008134-1A_H3TGMDSX7_S1_L001_R1_001.fastq.gz \ --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN \ # --set-cell-number=100 \ --log2stderr > whitelist.txt # Step 2: Extract barcdoes and UMIs and add to...
whitelist 命令会从原始数据种提取去可能的cell barcode。通常情况下,10X的barcode长度为16nt,umi长度为12nt;Drop-seq的barcode长度为12nt,umi长度为8nt。示例代码如下: #10X umi_tools whitelist --stdin hgmm_100_R1.fastq.gz \ --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNNNN \ --set-cell-number=100 \ -...
该存储库包含用于处理唯一分子标识符(UMI)/随机分子标签(RMT)和单细胞RNA-Seq细胞条形码的工具。 当前有6个命令。 extract和whitelist命令用于准备包含uMI的fastq +/-细胞条形码以进行对齐。 白名单: 建立“真实”细胞条形码的白名单 对于真正细胞条形码的身份未知的基于液滴的单细胞RNA-Seq,这很有用。 然后,白名单...
whitelist: Builds a whitelist of the 'real' cell barcodes This is useful for droplet-based single cell RNA-Seq where the identity of the true cell barcodes is unknown. Whitelist can then be used to filter with extract (see below)
whitelist: Builds a whitelist of the 'real' cell barcodes This is useful for droplet-based single cell RNA-Seq where the identity of the true cell barcodes is unknown. Whitelist can then be used to filter with extract (see below)
whitelist 命令会从原始数据种提取去可能的cell barcode。通常情况下,10X的barcode长度为16nt,umi长度为10nt;Drop-seq的barcode长度为12nt,umi长度为8nt。示例代码如下: umi_tools whitelist--stdinhgmm_100_R1.fastq.gz \--bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN \--set-cell-number=100\--log2stderr>white...
elif [ $TEST_FUNCTIONALITY ] ; then nosetests -v tests/test_umi_tools.py ; elif [ $TEST_HELP ] ; then umi_tools whitelist --help; umi_tools extract --help; umi_tools group --help; umi_tools dedup --help; umi_tools count --help; umi_tools count_tab --help; fi©...
whitelist: Builds a whitelist of the 'real' cell barcodes This is useful for droplet-based single cell RNA-Seq where the identity of the true cell barcodes is unknown. Whitelist can then be used to filter with extract (see below)