AI代码解释 -b # 输入bam文件-o # 输出-p # 线程数-e/--extendReads # 拓展了原来的read长度-bs/--binSize # 设置分箱的大小--filterRNAstrand{forward,reverse}:仅统计指定正链或负链--region/-rCHR:START:END:选取某个区域统计 #为了其他结果进行比较,还需要进行标准化,deepto
I'm using the latest deeptools available in conda (bamCoverage 2.5.7), but the same is true for my previous deeptools version (2.2.4). $ bamCoverage \ --bam GR.dedup_filtered.sorted.bam \ --binSize 1 \ --verbose \ --extendReads 200 \ --normalizeUsingRPKM \ --outFileFormat big...
Tools to process and analyze deep sequencing data. - deepTools/docs/content/tools/bamCoverage.rst at 2.4.1 · deeptools/deepTools
-e/--extendReads# 拓展了原来的read长度 -bs/--binSize# 设置分箱的大小 --filterRNAstrand {forward, reverse}: 仅统计指定正链或负链 --region/-r CHR:START:END: 选取某个区域统计 #为了其他结果进行比较,还需要进行标准化,deeptools提供了如下参数: --scaleFactor: 缩放系数 --normalizeUsing {RPKM,CP...
Full size image To test the potential ofBAMscaleRNA-seq mode, we reprocessed previously published RNA-seq data fromTop1mtwild type and knock-out mice [38].BAMscaleis capable of producing more accurate, single-base resolution tracks at exon–intron boundaries, compared toIGVToolsordeepTools bamC...
conda install deeptools 二、bamCoverage的用法 安装完成以后,可以使用bamCoverage -h来查看软件的帮助文档。 1. 软件用法: image-20210505115314404 2.常用参数: -b# 输入bam文件 -o# 输出 -p# 线程数 -e/--extendReads# 拓展了原来的read长度 -bs/--binSize# 设置分箱的大小 ...
.. argparse:: :ref: deeptools.bamCoverage.parseArguments :prog: bamCoverage Usage hints A smaller bin size value will result in a higher resolution of the coverage track but also in a larger file size. The 1x normalization (RPGC) requires the input of a value for the effective genome ...