User: fing

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fing0
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Posts by fing

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Comment: C: cuffdiff splicing.diff 'notest' - interpretation?
... Thanks - this makes sense, good to know the output isn't too weird, and after having a look at some of the data it seems to  make sense. ...
written 3.4 years ago by fing0
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cuffdiff splicing.diff 'notest' - interpretation?
... Hi everyone, I guess this is more of a general query about interpretation of cuffdiff output, since (thanks to some help from biostars) I'm pretty happy that my analysis is running correctly. I hope someone will be happy to help (again) as I'm an RNA-seq newbie. I have ran cuffdiff on a set of RNA ...
interpretation splicing cufflinks cuffdiff written 3.4 years ago by fing0
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Comment: C: cufflinks splicing analysis drosophila - 'notest' in output
... Hi again, and a big thank you because you have fixed this issue for me. Your point (3) did the job, the filtered .gff allows tests to run where the unfiltered version would not. As you suspected, cufflinks called gffread without prompt. Best, Fiona ...
written 3.4 years ago by fing0
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Comment: C: cufflinks splicing analysis drosophila - 'notest' in output
... Hi, thanks for your reply. I guess it would make sense if there was something wrong with my reference file, and as this is the first time I used cuffcompare, it's possible my mistake is here. I was trying to follow instructions I found on a cufflinks helppage (http://cole-trapnell-lab.github.io/cuff ...
written 3.4 years ago by fing0
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cufflinks splicing analysis drosophila - 'notest' in output
... Hi everyone, I'm attempting to use cufflinks to examine alternative splicing in my RNAseq data from drosophila. I'm new to the analysis and running into some problems, I'd really appreciate any help offered. I aligned my data to the dm6 reference genome from UCSC, using the R/BioConductor platform ...
drosophila splicing cufflinks written 3.4 years ago by fing0
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Comment: C: Getting Annotation Data From A Gff File
... Hi, I compared the lengths of each side of the assignment: length(seqlengths(gff)) [1] 1871 length(end(ranges(gff[which(elementMetadata(gff)[,"type"]=="chromosome"),]))) [1] 2 Obviously this makes the error message in itself very clear, but I'm not sure what information I need to figure out th ...
written 3.7 years ago by fing0
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Comment: C: Getting Annotation Data From A Gff File
... Hi, I am having the same problem with very similar code (that I learnt in a BioC RNAseq workshop). My code is: gff <- import.gff("dmel-all-r6.05.gff.gz", asRangedData=F) seqlengths(gff) <- end(ranges(gff[which(elementMetadata(gff)[,"type"]=="chromosome"),])) I then get the same error mes ...
written 3.8 years ago by fing0

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