每个GEM well是10X芯片上的一个单独的区室,从barcode池 (barcode whitelist,前面--qc的结果中有,评估barcode测序准确度,进而影响细胞鉴定准确度)中随机获取barcode用于标记细胞。为了保证整合多个文库时barcode不发生冲突,通常会在barcode后面加一个数字,标记其来源的GEM well,如AGACCATTGAGACTTA-1和AGACCATTGAGACTTA-2...
Answer: A barcode whitelist is the list of all known barcode sequences that have been included in the assay kit and are available during library preparation. For example, there are roughly 737,000 cell barcodes in the whitelist for 5' v2 chemistry. Here are the first 10 lines of the corr...
每个GEM well是10X芯片上的一个单独的区室,从barcode池 (barcode whitelist,前面--qc的结果中有,评估barcode测序准确度,进而影响细胞鉴定准确度)中随机获取barcode用于标记细胞。为了保证整合多个文库时barcode不发生冲突,通常会在barcode后面加一个数字,标记其来源的GEM well,如AGACCATTGAGACTTA-1和AGACCATTGAGACTTA-2...
黑色->紫色:umi_tools whitelist, wash_whitelist, umi_tools extract 黑色阴影:Reads with Non-correctable Reads, invalid Barcode & UMI (discarded) 紫色:Barcode有效的Reads(Reads with valid Barcode & UMI) 紫色->黄色:STAR 紫色阴影:Reads NOT Unique Mapped to Genome (discarded) 黄色:Unique Mapped Reads...
[error] Unable to auto-detect chemistry. Sample def 0/Pool111-2_23: Fraction of barcodes on whitelist was at best 1.3 1%, while we expected at least 10.00% for one of the chemistries. 确定了是试剂盒的问题,用的不是正常的10x试剂盒。
Each GEM well is a physically distinct set of GEM partitions that draws barcode sequences randomly from the pool of valid barcodes cataloged in thebarcode whitelist. To track barcodes when aggregating multiple libraries, Cell Ranger appends an integer identifying the GEM Well to the barcode nucleo...
Each GEM well is a physically distinct set of GEM partitions, but draws barcode sequences randomly from the pool of valid barcodes, known as thebarcode whitelist. To keep the barcodes unique when aggregating multiple libraries, we append a small integer identifying the GEM well to the barcode...
I am testing a dataset with follow Fastq header and Reads structure, but cellranger count complains "an extremely low rate of correct barcodes was observed for this chemistry", It seems that cellranger do not support my data, how can I add DEFINED library information in cellranger count?
The situation about those cell barcode whitelists is a bit more complicated than usual. You can check the preprocessing tutorial page for more information about where those files come from and how to use them.</info> 12 12 13 13 <info>IMPORTANT: Thank @dannyconrad for pointing out the...
=len(barcode_set):raiseException(f"Duplicates found in barcode whitelist:{filename}")returnbarcode_setifas_setelsebarcodes 功能: 加载条形码白名单文件,返回条形码列表或集合。 参数: filename(字符串或字节串): 白名单文件路径,可以是.txt或.txt.gz格式。