RSEM是用于计算转录组测序数据表达量的工具。它的用法如下: 1. 首先,使用Bowtie或Bowtie2将原始数据与转录本序列进行比对。 2. RSEM根据比对结果计算表达量。 3. 输入构建好索引的转录本参考文件(由分析模块“Build Transcript Reference Index”生成)以及转录组测序原始数据(fastq文件)。 4. RSEM将转录组测序原始...
STAR+RSEM 先比对再进行定量 # build index 建立索引; STAR --runThreadN 10 --runMode genomeGenerate \ --genomeDir arab_STAR_genome \ --genomeFastaFiles 00ref/TAIR10_Chr.all.fasta \ --sjdbGTFfile 00ref/Araport11_GFF3_genes_transposons.201606.gtf \ --sjdbOverhang 149 # 一般为read...
Build References 这步可以理解为是对转录本建索引,RSEM支持两种方式: 第一种是提供参考基因组fa序列和GTF注释文件,那么RSEM则会通过GTF注释文件从参考基因组序列中提取出各个转录本的序列,然后利用Bowtie2 or STAR等软件来建索引 ~/biosoft/rsem/RSEM-1.3.0/rsem-prepare-reference -gtf ~/annotation/hg38/gencod...
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/usr/bin/convert-sam-for-rsem /usr/bin/extract-transcript-to-gene-map-from-trinity /usr/bin/rsem-bam2readdepth /usr/bin/rsem-bam2wig /usr/bin/rsem-build-read-index /usr/bin/rsem-calculate-credibility-intervals /usr/bin/rsem-calculate-expression /usr/bin/rsem-control-fdr /usr/bin/rsem-...
buildReadIndex.cpp calcCI.cpp cnt_file_description.txt convert-sam-for-rsem extract-transcript-to-gene-map-from-trinity extractRef.cpp getUnique.cpp model_file_description.txt my_assert.h parseIt.cpp preRef.cpp rsem-calculate-expression
# build index 建立索引;STAR--runThreadN10--runMode genomeGenerate \--genomeDir arab_STAR_genome \--genomeFastaFiles00ref/TAIR10_Chr.all.fasta \--sjdbGTFfile00ref/Araport11_GFF3_genes_transposons.201606.gtf \--genomeSAindexNbases12\--sjdbOverhang149# 一般为reads长度-1(150-1) ...
用法:hisat2-build [options]*<reference_in><ht2_index_base> <reference_in>是参考基因组或者参考转录本的路径,<ht2_index_base>是输出的索引文件所在的目录以及前缀。[options]*指一些其他可选参数,为-p指定线程数可以加快构建索引的速度,其他参数默认既可。
(Default: off) --sort-bam-by-coordinate Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices. (Default: off) --sort-bam-memory <string> Set the maximum memory per thread that can be used by 'samtools sort'. <string> represents the memory and acce...
Normally, RSEM will do this for you via--output-genome-bamoption ofrsem-calculate-expression. However, if you have runrsem-prepare-referenceand usereference_name.idx.fato build indices for your aligner, you can usersem-tbam2gbamto convert your transcript coordinate BAM alignments file into a ge...