RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - bioinfo-fiend/rnaseq
NH:i:后面的数值代表着此条read比对到几个loci,1代表着unique map,数值大于1代表着multi-mappers HI:i:后面的数值attrbiutes enumerates multiple alignments of a read starting with 1,下游分析接cufflinks or stringtie的时候需要使用参数--outSAMattrIHstart 0 AS:i:的数值代表着local alignment score (paired...
HiSAT2 -> NO QUANTIFICATION Sort and index alignments (SAMtools) UMI-based deduplication (UMI-tools) Duplicate read marking (picard MarkDuplicates) Transcript assembly and quantification (StringTie) Create bigWig coverage files (BEDTools, bedGraphToBigWig) Extensive quality control: RSeQC Qualimap dup...
0 may be required by some downstream software, such as Cufflinks or StringTie. outSAMunmapped None string(s): output of unmapped reads in the SAM format 1st word: None ... no output Within ... output unmapped reads within the main SAM file (i.e. Aligned.out.sam) 2nd word: KeepPairs...
我们来看一下最后面的 NH:i:1HI:i:1AS:i:289nM:i:0NH:i:后面的数值代表着此条read比对到几个loci,1代表着unique map,数值大于1代表着multi-mappersHI:i:后面的数值attrbiutes enumerates multiple alignmentsofa read startingwith1,下游分析接cufflinksorstringtie的时候需要使用参数--outSAMattrIHstart0AS:...
(d) 不基于比对, 直接定量流程 Reference transcript HISAT2 Reads Sailfish/kallisto Stringtie /Salmon-SMEM /Salmon-Quasi Alignment-free isoform quantification counting Trinotate Trinotate 有参不比对转录组分析流程 Differential Enrichment Sequencing Gene quantification expression analysis RNA-seq Salmon reads DE...
HI:i:后面的数值attrbiutes enumerates multiple alignments of a read starting with 1,下游分析接cufflinks or stringtie的时候需要使用参数--outSAMattrIHstart 0 AS:i:的数值代表着local alignment score (paired for paired-edn reads) nM:i:的数值代表着the number of mismatches per (paired) alignment, ...
(d) 不基于比对 , 直接定量流程 Reference transcript HISAT2 Reads Sailfish/kallisto Stringtie /Salmon-SMEM /Salmon-Quasi Alignment-free isoform quantification counting Trinotate Trinotate 易 有参不比对转录组分析流程 生 信 Differential Enrichment Sequencing Gene quantification expression analysis RNA-seq ...
HiSAT2 -> NO QUANTIFICATION Sort and index alignments (SAMtools) UMI-based deduplication (UMI-tools) Duplicate read marking (picard MarkDuplicates) Transcript assembly and quantification (StringTie) Create bigWig coverage files (BEDTools, bedGraphToBigWig) Extensive quality control: RSeQC Qualimap dup...
HiSAT2 -> NO QUANTIFICATION Sort and index alignments (SAMtools) UMI-based deduplication (UMI-tools) Duplicate read marking (picard MarkDuplicates) Transcript assembly and quantification (StringTie) Create bigWig coverage files (BEDTools, bedGraphToBigWig) Extensive quality control: RSeQC Qualimap dup...