User: jingjin2203

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jingjin220340
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Posts by jingjin2203

<prev • 34 results • page 1 of 4 • next >
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IsoformSwitchAnalyzeR - error in creating aSwitchList
... Hi All, I have been trying to use IsoformSwitchAnalyzeR (1.6.0) to analyze my RNAseq data. I followed the tutorial but encountered some issue (code and error attached below). I was wondering if anyone could help me fix it? I also had a question about which gtf file should be used as isoformExonAnn ...
isoformswitchanalyzer rna-seq written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... Thanks, Kristoffer! Will do. And yes, I have IsoformSwitchAnalyzeR 1.6.0 installed. ...
written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... I read ?importRdata in R, it says isoformExonAnnoation can either be "A string indicating the full path to the (gziped or unpacked) GTF file which have been quantified". What is a quantified GTF file? ...
written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... Hi Kristoffer, sorry for keeping bugging you. I have successfully generated ctab files for each of my samples following your advice. I tried to analyze the data using IsoformSwitchAnalyzeR, but encountered some issue. I was wondering if you could help me fix it? I also had a question about which gtf ...
written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... This is really helpful!! Thank you so much for help!! ...
written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... Thanks a lot for your help! Really appreciated it! Just wanted to make sure I understand everything correctly, since my goal is to detect novel transcripts, -e (only estimate the abundance of given reference transcripts) should not be used, is that correct? Sorry about the silly questions, thanks a ...
written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... Thank you, Kristoffer! So, basically the process would be same for identifying novel transcripts and DEGs, is that correct? ...
written 8 weeks ago by jingjin220340
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Comment: C: RNAseq - how to find novel transcripts in under different treatment using string
... Thank you for your kind help! Really appreciated it! Do I have to use DESeq2 to get transcript count tables? ...
written 9 weeks ago by jingjin220340
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RNAseq - how to find novel transcripts in under different treatment using stringTie and gffcompare?
... Hi all, I was wondering how to find novel transcripts under different treatment conditions using stringTie? I have 4 different treatments and 3 replications for each of the treatments in my RNAseq data. I have tried to merge the 12 gtf files generated by stringTie and compared the merged gtf to th ...
rna-seq transcripts written 9 weeks ago by jingjin220340 • updated 9 weeks ago by rmash0
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Comment: C: RNAseq raw read counts for measuring relative gene expression?
... I think I understand why within-sample differential gene expression analysis is not possible after TMM because gene length normalization is skipped. Without gene length normalization, the relative quantification of the expression level of gene of interest to "internal control" gene would not be accu ...
written 3 months ago by jingjin220340

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