转录本拼装和可变剪接瑞客

转录本拼为什么转录本可以拼接起 有参组装和无参 有参转录组分析流程–可变剪 RR可变剪接分

StringTieisafastandhighlyefficientassemblerofRNA-Seqalignmentsintopotentialtranscripts.Itusesanovelnetworkflowalgorithmaswellasanoptionaldenovoassemblysteptoassembleand tatefull-lengthtranscriptsrepresentingmultiplesplicevariantsforeachgenelocus.Itsinputcanincludenotonlythealignmentsofrawreadsusedbyothertranscriptassemblers,butalsoalignmentslongersequencesthathavebeenassembledfromthosereads.Inordertoidentifydifferentiallyexpressedgenesbetweenexperiments,StringTie'soutputcanbeprocessedbyspecializedsoftwarelikeBallgown,Cuffdifforotherprograms(DESeq2,edgeR,etc.). 地址-进入文 获得当前工 当前工 - - - - - stringtie--merge-p1-GGRCh38.gtf-lehbio_trans-ostringtie_merged.gtfmergelist.txt#merge模式，amergedGTFfilefromasetofGTFfiles, stringtie-G -lsampleA-f0.15-p1-e-B-sampleA/sampleA.stringtie_quant.gtf从拼装定量的gtf文件整理 table（也可用count或featureCount计算获得）， prepDE.py-isample_lst.txt-g#sample_lst.txt包括sample的名称和定gtf所在的路 Theprogramparecanbeusedtocompare,merge,annotateandestimateaccuracyofoneormoreGFFfiles(the“query”files),whencomparedwithareferenceannotation.pare-R-rGRCh38.gtf-osampleA2GRCh38-i 输出文计)sampleA2GRCh38.sampleA.stringtie_first.gtf.tmap(最匹配的原注释与装转录本的匹配信sampleA2GRCh38.loci(转录本 组上的坐标信息 Ifparewasrunwiththe-roption(paringwithareferenceannotation),trackingrowswillcontaina"classcode"valueshowingtherelationshipbetweenatransfragandtheclosestreferencetranscript(whereapplicable).Ifthe-roptionwasnotusedtherowswillallcontain“-”intheirclasscodecolumn.Thesamecodesarealsoshownasthevalueoftheattribute"class_code"intheoutputGTFfile.Theclasscodesareshownbelowindecreasingorderoftheirpriority.组装转录本与参考转录本之间的匹配类 潜在

位于内含子内含子包含参聚合酶通读 可变剪接分可变的3信，毕生缘；培训 样品特异的选择性剪 的鉴信，毕生缘；培训 tar-xzfrMATS.4.0.2.tgzcd guide.htm(userguidestepPre-InstallPython2.7.xandcorrespondingversionsofNumPyandSciPyDownloadandinstallpysam(rMATSwastestedwithv)Downloadandinstallsamtools(version1.2orlater)DownloadandinstallSTAR(version2.5or信，毕生缘；培训 pipinstallnumpy--pipinstallscipy--timeout=1000--user#(网 速度较慢时可设置-pipinstallpysam--信，毕生缘；培训 WhichversiontoOpenpythonconsoleandtype>>>import>>>printThisoutputindicatesthatyourpythonisbuiltwith--enable->>>import>>>printThisoutputindicatesthatyourpythonisbuiltwith--enable-unicode=ucs2,andyoushoulduserMATS-turbo-xxx-UCS2.信，毕生缘；培训 s1.txt和s2.txt是以s1.txt和s2.txt是以逗号分b1.txt和b2.txt是以逗号隔的样本bam文paired，单端测序为为-treadType双端reads的长gtf注释文输入文件是fastq格式时指定STAR索引文件位 信，毕生缘；培训 pythonrMATS-turbo-xxx-UCSx/rmats.py--s1s1.txt--s2s2.txt--gtfgtfFile--biSTARindexFile--odout_directory-tpaired--nthread2--tstat2--readLength101--tophatAnchor8--cstat0.0001#输入文件是fastq格 rMATS-turbo-xxx- -- -- - readLength101--cstat0.0001--libTypefr-unstranded

-- -信，毕生缘；培训 evaluatessplicingwithonlyreadsthatspansplicingevaluatessplicingwithreadsthatspansplicingjunctionsandreadsonallpossiblealternativesplicing(AS)eventsderivedfromGTFandevaluatessplicingwithonlyreadsthatspansplicingevaluatessplicingwithreadsthatspansplicingjunctionsandreadson信，毕生缘；培训 rMATS输出结果解信，毕生缘；培训 rMATS输出结果每列 信，毕生缘；培训 rMATS输出结果每列 生缘；培训 outputintosashimiplotPython2.6.xorPython2.7.xInstall index unziprmats2sashimiplot-cdrmats2sashimiplot-masterpythonsetup.py或者利用pip进行安 逗号分隔的样本逗号分隔的样本-t-e-e--l1--l1和--l2：第一组和 rmats2sashimiplot--s1 - - -sampleB--exon_s1--intron_s5-o#输入文件是sam格

-- sampleA-- rmats2sashimiplot--b1sampleA.R1.bam,sampleA.R2.bam,sampleA.R3.bam- - :.gff3File--l1sampleA--l2sampl