转录组分析流程salmon瑞客

(d)不基于比对，

&易om生信e，b毕io生lo缘g；y.培b训io版m权e所d有c xx

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FASTQqualityscores=ASCIIqualityscore-either33or Illumina e=estimatedprobabilityofthebasecallbeingwrongQ40:1errorin10,000basecalls;Q30:1errorin1,000;Q28:1.6errorin1000;Q25:3errorin1000;Q20:1errorin信，毕生缘；培训 FASTQ CDNA (.fa (.gtf xx 信，毕生缘；培训 公共数据从NCBISRA使用NCBI提供的SRA-toolkit中的工具fastq-dump直接SRR文件，并转换双端就自动拆分，如果是单端不受的数据集一般比较大，放入 (nohupcmd&)。nohupfastq-dump-v--split-3--nohup&fastq-dump-v--split-3--& 77 fastqc x-axis:Positionin y-axis:Quality信，毕生缘；培训 (箱线图通过最大值、上四分位示质量得分。将所有reads的第一位碱基质量得分进行箱线 信，毕生缘；培训 信，毕生缘；培训 每个readGC含量的分布图。横坐标表示平均GC含量，纵坐标表示reads数。左图显示每个read的GC分布(红线)与理论分布(蓝线)相契合，GC含量均一。右图出现了GC含量双峰，表示样品可能存在特定的序列污染如混入了引物二聚体，当这一信，毕生缘；培训 ../FastQC/Configuration/adapter_list.txtFastQC工具会与这两个文件里的序列进行比信，毕生缘；培训 信，毕生缘；培训 直方图展示有 量异常高或低的样本 横轴是GC含量的判断，纵轴是碱基横轴表 reads数，纵轴表示给定 数区间内样本数目，即给 深度有多 样本 reads数低于20M的样品没有， 高于40M

信，毕生缘；培训 接头和低质量readsmCommondjava-jartrimmomatic-0.30.jarPE--phred33input_forward.fqinput_reverse.fqoutput_forward_paired.fqoutput_forward_unpaired.fqoutput_reverse_paired.fqoutput_reverse_unpaired.fqILLUMINACLIP:adaptor-PE.fa:2:30:10LEADING:20TRAILING:20MINLEN:36TwoinputfilesandfouroutputRemoveadapters:( um2mismatchesinthe'seed'(16bases)oftheadaptor;palindromeclipthreshold30;simpleclipthreshold10)Removeleadinglowqualitybases(belowquality20);Removetrailinglowqualitybases(belowquality20);Dropreadsbelowthe36base易s生信lo，n毕 (2x(2x150(.fastq

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(.gtf 信，毕生缘；培训 Ensembl(信，毕生缘；培训E。nsemblcDNA指编 的 RNA- GTF(GeneTransferFormat, RNA- CDNA(.faCDNA(.fa(2x150(.fastq 易s生c信.，e毕d生u缘/F；A培Q训版/F权A所Q有 m1-seqname-nameofthechromosomeorscaffold;chromosomenamescanbegivenwithorwithoutthe'chr'prefix.Importantnote:theseqnamemustbeoneusedwithinEnsembl,i.e.astandardchromosomenameoranEnsemblidentifiersuchasascaffoldID,withoutanyadditionalcontentsuchasspeciesorassembly.SeetheexampleGFFoutputbelow.m2-source-nameoftheprogramthatgeneratedthisfeature,orthedatasource(databaseorprojectname)m3-feature-featuretypename,e.g.Gene,Variation, 4-start-Startpositionofthefeature,withsequencenumberingstartingat1. 5-end-Endpositionofthefeature,withsequencenumberingstartingat1. 6-score-Afloatingpointvalue. 7-strand-definedas+(forward)or- 8-frame-Oneof'0','1'or'2'.'0'indicatesthatthefirstbaseofthefeatureisthefirstbaseofacodon,'1'thatthesecondbaseisthefirstbaseofacodon,andsoon.. 9-attribute-Asemicolon-separatedlistoftag-valuepairs,providingadditional6612信，毕生缘；培训 bed–至少3列，另外9列可选，0-start信，毕生缘；培训 信，毕生缘；培训

- (.gtffile)(.gtffile)(.fafile)(.fastqx RNA- A transcripts_index--typequasi-k <LIBTYPE>-1reads1.fq-2reads2.fqo2 定量时考虑到不同样品 长度的改变（比如不同 g易n生e信t，te毕s生/缘D；E培训S版e权q所2有/。 (.fafile)(.fastqx(.fafile)(.fastqx RNA- (.gtf 信，毕生缘；培训 (.fafile)(.fafile)(.fas