3 umi_tools extract [OPTIONS] -p PATTERN [-I IN_FASTQ[.gz]] [-S OUT_FASTQ[.gz]] --read2-in=IN2_FASTQ[.gz] --read2-out=OUT2_FASTQ[.gz] umi_tools extract --whitelist=/home/lizhixin/softwares/cellranger-7.0.1/lib/python/cellranger/barcodes/3M-february-2018.txt --stdin=HT29_...
extract命令会从fastq文件中提取包含可接受barcode的reads,默认情况下extract命令会忽略umi的reads质量情况而不做处理。示例代码如下: umi_tools extract--bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN \--stdinhgmm_100_R1.fastq.gz \--stdouthgmm_100_R1_extracted.fastq.gz \--read2-in hgmm_100_R2.fastq.gz \...
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...
umi_tools extract will do this if you add --read2-in and --read-out options to the call. By default it is assumed that the UMI is only found on read one. Read1, trimmed of the UMI will be output, but you can just discard this and only map read2, which should now have the ...
Theextractandwhitelistcommands are used to prepare a fastq containg UMIs +/- cell barcodes for alignment. 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 th...
之前拿到了一组类似Drop-seq的序列,虽然是双端测序,但只有read2用作映射参考基因,read1只提供cell barcode+UMI用于后期去重。需要对序列匹配到同一个基因且拥有同样cell barcode的唯一UMI进行计数。于是就要用到UMI-tools的count命令。 Drop-seq的原理可以看文章Highly Parallel Genome-wide Expression Profiling of Ind...
extract命令会从fastq文件中提取包含可接受barcode的reads,默认情况下extract命令会忽略umi的reads质量情况而不做处理。示例代码如下: umi_tools extract--bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN \--stdinhgmm_100_R1.fastq.gz \--stdouthgmm_100_R1_extracted.fastq.gz \--read2-in hgmm_100_R2.fastq.gz \...
Also, the new --umi-separator command to umi-tools extract will be beneficial. So far only available for umi-tools dedup, so we had to stick to underscores as separator, although Illumina's bclconvert imposes a semicolon. PR checklist This comment contains a description of changes (with rea...
Several techniques that use UMIs mix the UMI sequence in with a library barcode. In this case we want to remove the random part of the barcodes, but leave the library part so that the reads can be de-multiplexed. We specify this using the--bc-patternparameter toextract. Ns r...