User: ruansun1983

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ruansun198330
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United States
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4 years, 11 months ago
Joined:
6 years ago
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about me

Posts by ruansun1983

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
... RUM require read1 and read2 files have exactly the same file size. So I have to refill trimmed reads with N after quality control with Prinseq, which is a stupid step .  I think it is not necessary. RUM author should consider to remove this restriction. ...
written 4.9 years ago by ruansun198330
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Comment: C: RNA-seq GC content Bimodal distribution
... I don't know how to post image. But added a link to the picture ...
written 4.9 years ago by ruansun198330
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Comment: C: tophat2 stopped at bowtie step
... Just tried, not work, the same error ...
written 4.9 years ago by ruansun198330
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RNA-seq GC content Bimodal distribution
... Is it normal for RNA-seq from human to have bimodal distribution in GC content? For DNA seq bimodal distribution in GC content is a sign of contamination. How about RNA-seq? http://postimg.org/image/nrlw7wgdf/ ...
rna-seq written 4.9 years ago by ruansun198330 • updated 19 months ago by from the mountains40
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Answer: A: Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
... It is much more easier and friendly to install/use than tophat.  The status check of RUM is also very friendly designed. You can know very easily what it is doing and is there any error. didn't test the performance yet, but will do it soon.    ...
written 5.0 years ago by ruansun198330
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Comment: C: tophat2 stopped at bowtie step
... just tried, does not work. the same error ...
written 5.0 years ago by ruansun198330
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Comment: C: Installation Of Tophat -1.1.4
... No matter how I try, It alway complain this stupid error. Have switched to RUM for RNA-seq ...
written 5.0 years ago by ruansun198330
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Comment: C: tophat2 stopped at bowtie step
... original quality score report the same error. That is why I convert it ...
written 5.0 years ago by ruansun198330
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tophat2 stopped at bowtie step
... Here is the problem I have two paired read files, each with only 250 reads (so memory is not an issue) the quality score is in illumina 1.8 format, has concerted to illumina 1.3 with command sed -ie '4~4y/!"#$%&'\''()*+,-.\/0123456789:;<=>?@ABCDEFGHIJ/@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`a ...
tophat written 5.0 years ago by ruansun198330 • updated 5.0 years ago by Jordan1.1k
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Comment: C: How Illumina Methylation Array Find Out Whether It Is A Tg In Original Sample
... You didn't quite understand my question. I mean how can they make sure the site is CpG, not TpG in specific sample? ...
written 6.0 years ago by ruansun198330

Latest awards to ruansun1983

Student 4.9 years ago, asked a question with at least 3 up-votes. For RNA-seq GC content Bimodal distribution

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