轉(zhuǎn)錄本拼裝和可變剪接瑞客

轉(zhuǎn)錄本拼為什么轉(zhuǎn)錄本可以拼接起 有參組裝和無參 有參轉(zhuǎn)錄組分析流程–可變剪 RR可變剪接分

StringTieisafastandhighlyefficientassemblerofRNA-Seqalignmentsintopotentialtranscripts.Itusesanovelnetworkflowalgorithmaswellasanoptionaldenovoassemblysteptoassembleand tatefull-lengthtranscriptsrepresentingmultiplesplicevariantsforeachgenelocus.Itsinputcanincludenotonlythealignmentsofrawreadsusedbyothertranscriptassemblers,butalsoalignmentslongersequencesthathavebeenassembledfromthosereads.Inordertoidentifydifferentiallyexpressedgenesbetweenexperiments,StringTie'soutputcanbeprocessedbyspecializedsoftwarelikeBallgown,Cuffdifforotherprograms(DESeq2,edgeR,etc.). 地址-進(jìn)入文 獲得當(dāng)前工 當(dāng)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從拼裝定量的gtf文件整理 table（也可用count或featureCount計(jì)算獲得）， prepDE.py-isample_lst.txt-g#sample_lst.txt包括sample的名稱和定gtf所在的路 Theprogramparecanbeusedtocompare,merge,annotateandestimateaccuracyofoneormoreGFFfiles(the“query”files),whencomparedwithareferenceannotation.pare-R-rGRCh38.gtf-osampleA2GRCh38-i 輸出文計(jì))sampleA2GRCh38.sampleA.stringtie_first.gtf.tmap(最匹配的原注釋與裝轉(zhuǎn)錄本的匹配信sampleA2GRCh38.loci(轉(zhuǎn)錄本 組上的坐標(biāo)信息 Ifparewasrunwiththe-roption(paringwithareferenceannotation),trackingrowswillcontaina"classcode"valueshowingtherelationshipbetweenatransfragandtheclosestreferencetranscript(whereapplicable).Ifthe-roptionwasnotusedtherowswillallcontain“-”intheirclasscodecolumn.Thesamecodesarealsoshownasthevalueoftheattribute"class_code"intheoutputGTFfile.Theclasscodesareshownbelowindecreasingorderoftheirpriority.組裝轉(zhuǎn)錄本與參考轉(zhuǎn)錄本之間的匹配類 潛在

位于內(nèi)含子內(nèi)含子包含參聚合酶通讀 可變剪接分可變的3信，畢生緣；培訓(xùn) 樣品特異的選擇性剪 的鑒信，畢生緣；培訓(xùn) tar-xzfrMATS.4.0.2.tgzcd guide.htm(userguidestepPre-InstallPython2.7.xandcorrespondingversionsofNumPyandSciPyDownloadandinstallpysam(rMATSwastestedwithv)Downloadandinstallsamtools(version1.2orlater)DownloadandinstallSTAR(version2.5or信，畢生緣；培訓(xùn) pipinstallnumpy--pipinstallscipy--timeout=1000--user#(網(wǎng) 速度較慢時(shí)可設(shè)置-pipinstallpysam--信，畢生緣；培訓(xùn) WhichversiontoOpenpythonconsoleandtype>>>import>>>printThisoutputindicatesthatyourpythonisbuiltwith--enable->>>import>>>printThisoutputindicatesthatyourpythonisbuiltwith--enable-unicode=ucs2,andyoushoulduserMATS-turbo-xxx-UCS2.信，畢生緣；培訓(xùn) s1.txt和s2.txt是以s1.txt和s2.txt是以逗號(hào)分b1.txt和b2.txt是以逗號(hào)隔的樣本bam文paired，單端測(cè)序?yàn)闉?treadType雙端reads的長(zhǎng)gtf注釋文輸入文件是fastq格式時(shí)指定STAR索引文件位 信，畢生緣；培訓(xùn) pythonrMATS-turbo-xxx-UCSx/rmats.py--s1s1.txt--s2s2.txt--gtfgtfFile--biSTARindexFile--odout_directory-tpaired--nthread2--tstat2--readLength101--tophatAnchor8--cstat0.0001#輸入文件是fastq格 rMATS-turbo-xxx- -- -- - readLength101--cstat0.0001--libTypefr-unstranded

-- -信，畢生緣；培訓(xùn) evaluatessplicingwithonlyreadsthatspansplicingevaluatessplicingwithreadsthatspansplicingjunctionsandreadsonallpossiblealternativesplicing(AS)eventsderivedfromGTFandevaluatessplicingwithonlyreadsthatspansplicingevaluatessplicingwithreadsthatspansplicingjunctionsandreadson信，畢生緣；培訓(xùn) rMATS輸出結(jié)果解信，畢生緣；培訓(xùn) rMATS輸出結(jié)果每列 信，畢生緣；培訓(xùn) rMATS輸出結(jié)果每列 生緣；培訓(xùn) outputintosashimiplotPython2.6.xorPython2.7.xInstall index unziprmats2sashimiplot-cdrmats2sashimiplot-masterpythonsetup.py或者利用pip進(jìn)行安 逗號(hào)分隔的樣本逗號(hào)分隔的樣本-t-e-e--l1--l1和--l2：第一組和 rmats2sashimiplot--s1 - - -sampleB--exon_s1--intron_s5-o#輸入文件是sam格

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