10 请问老师有根据基因ID一次性提取UTR,EXON,INTRON的脚本吗?

组学大讲堂基因家族分析课程里给的脚本貌似只能提取EXON和INTRON,请问能给一个把UTR也提取出来的脚本吗?谢谢!

编程太菜,一时半会儿琢磨不出来 T_T|||


我试了组学大讲堂之前提供的一个脚本貌似不行,.....https://www.omicsclass.com/article/750

我只在esmbel下载的水稻和拟南芥的gff3文件,转录本ID应该也是对的。

attachments-2020-06-xbhe10MK5eedbdbbc3ea0.png

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6.20 更新

该问题已得到解决;我用TBTOOLS做了进化树,MOTIF以及基因结构的“三连图”(在一种物种中)。

但是我作的树包含了拟南芥和水稻两种物种,将gtf文件合并后作三连图却出现了一下报错,不知道为啥?

=========================================
==============A Big Warniing=============
=========================================
 IDs that you used as input do      
 NOT present in gff/gtf file.     
 Examples of valid IDs is showed as bellowed
Guess FileType is:GTF
transcript:AT1G03987.1
transcript:AT1G01020.6
transcript:AT1G01010.1
transcript:AT1G01020.3
transcript:AT1G01020.2
transcript:AT1G01020.5
transcript:AT1G01020.4
transcript:AT1G01020.1
transcript:AT1G01030.2
transcript:AT1G01030.1
transcript:AT1G01040.1
=========================================
六月 20, 2020 7:15:48 下午 biocjava.bioDoer.MEME.DrawMotifPattern.DrawGeneStructureFromGXFfile metaParser
严重: null
java.io.IOException: Parsing Gxf Error...See above...
at biocjava.bioDoer.MEME.DrawMotifPattern.DrawGeneStructureFromGXFfile.metaParser(DrawGeneStructureFromGXFfile.java:87)
at biocjava.bioDoer.MEME.DrawMotifPattern.DrawMotifPatternFromMEMEResult.postGraph(DrawMotifPatternFromMEMEResult.java:1020)
at biocjava.bioDoer.MEME.DrawMotifPattern.DrawAmazingMetaPlot.plot(DrawAmazingMetaPlot.java:617)
at biocjava.GUIexcutors.JIGplotToolkit.AmazingGeneViewGUIPanel$15$1.run(AmazingGeneViewGUIPanel.java:490)
六月 20, 2020 7:15:48 下午 biocjava.GUIexcutors.JIGplotToolkit.AmazingGeneViewGUIPanel$15$1 run
严重: null
java.lang.NullPointerException
at biocjava.bioDoer.MEME.DrawMotifPattern.DrawMotifPatternFromMEMEResult.postGraph(DrawMotifPatternFromMEMEResult.java:1029)
at biocjava.bioDoer.MEME.DrawMotifPattern.DrawAmazingMetaPlot.plot(DrawAmazingMetaPlot.java:617)
at biocjava.GUIexcutors.JIGplotToolkit.AmazingGeneViewGUIPanel$15$1.run(AmazingGeneViewGUIPanel.java:490)


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最佳答案 2020-06-21 00:09

已找到问题原因,转录本ID的问题  |||

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  • 苏麟-WSL 提出于 2020-06-19 21:31

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