withName:'.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP'{ publishDir=[ [ path: { params.save_align_intermeds||params.save_umi_intermeds?"${params.outdir}/${params.aligner}":params.outdir },
Runningumi_tools dedup --output-statsrequires a considerable amount of time and memory to generate the null distributions. If you want these stats, consider obtaining stats for just a single contig, eg.--chrom=chr22. If you are doing single-cell RNA-seq and you have reads from more ...
从fastq读取中灵活删除UMI序列。 删除了UMI,并将其附加到读取的名称之后。 任何其他条形码(例如库条形码)都保留在读取中。 也可以按质量或针对白名单过滤读取内容(请参见上文) 其余命令group , dedup和count / count_tab用于使用UMI识别PCR重复 所需:8积分电信网络下载...
UMI tools dedup to remove duplicates HTseq-count to summarize So far so good. Thanks for making UMI tools. It was the right tool at exactly the right moment for me. I lose a ton of reads (like 60-80% are duplicates), but that not the tool's fault. That's just the reality of ...
The remaining commands,group,dedupandcount/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user. A number of different UMI deduplication schemes are enabled - The recommended method isdirectional. ...
$ umi_tools dedup -I example.bam --output-stats=deduplicated -S deduplicated.bam The--output-statsoption is optional, but selecting it will provide a range of statistics about the run. One of the most interesting is the distribution of edit distances (here named deduplicated_edit...
dedup: Groups PCR duplicates and deduplicates reads to yield one read per group Use this when you want to remove the PCR duplicates prior to any downstream analysis group: Groups PCR duplicates using the same methods available through `dedup`. ...
The remaining commands,group,dedupandcount/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user. A number of different UMI deduplication schemes are enabled - The recommended method isdirectional. ...