STAR --genomeDir/home/lizhixin/project/scRNA-seq/GFP_YFP_tracing/reference/all.GFPs.ref \ --runThreadN 10 \ --readFilesIn 7Ala-D60-BO-2-1_S25_L003_R1_001.fastq.gz,7Ala-D60-BO-2-1_S25_L003_R2_001.fastq.gz UE-D60-BO-2-1_S21_L003_R1_001.fastq.gz,UE-D60-BO-2-1_S21_L00...
stringtie ${i}/${i}.Aligned.sortedByCoord.out.bam -G genome/GRCh38.gtf -l ${i} -o ${i}/${i}.stringtie_first.gtf -f 0.01 -p 1 done & # 转录本合并 cd ~/transcriptome/data # 获取所有拼装好的gtf文件 find . -name *.stringtie_first.gtf >mergeList.txt # -G: 指定reference GTF...
--readFilesCommand "gunzip -c" \ --outSAMstrandField intronMotif \ # include for potential use with StringTie for assembly --outSAMunmapped Within 包括以下与融合检测和STAR-Fusion执行相关的参数: --chimSegmentMin 12 \ # ** essential to invoke chimeric read detection & reporting ** --chimJunc...
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, n...
比对软件之STAR的使用方法 ⽐对软件之STAR的使⽤⽅法建索引 普通⽐对 ⼆次⽐对 ⽤于cufflinks和stringtie的⽐对 待续~参考：
--outSAMstrandField intronMotif \ # include for potential use with StringTie for assembly --outSAMunmapped Within Note, the "--twopassMode Basic" setting leads to data-set dependent behavior - ie., if you subsample your reads, there's no guarantee you'll find the same fusion even if the...
alignmentsofa read startingwith1,下游分析接cufflinksorstringtie的时候需要使用参数--outSAMattrIHstart0AS:i:的数值代表着local alignment score (pairedforpaired-edn reads)nM:i:的数值代表着the numberofmismatches per (paired) alignment,nottobe confusedwithNM, whichisthe numberofmismatchesineachmate ...
Stringtie requires the XS tag. The STAR manual (2.7.8a; I am running 2.7.6a) discusses its addition only in terms of Cufflinks/Cuffdiff. In a STAR v2.7.6a mapping run (one that was not gtf-guided -- I am treating the genome as not well-annotated) I have added the XS tag ...
(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...
(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 ...