User: rnaseql

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rnaseql0
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Posts by rnaseql

<prev • 5 results • page 1 of 1 • next >
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Comment: C: how to get counts/TPM/etc. from stringtie?
... Hi dec986, sorry to ask but did you manage to get Ballgown to run on the TPMs from StringTie? Thanks ...
written 7 days ago by rnaseql0
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Comment: C: Generating FPKM matrix accross all samples after stringtie
... Hello, apologies if I may have missed a post but would it be possible to obtain a isoform x sample matrix of TPM values from the output of StringTie to use for Ballgown? I would like to pass it as the 'gowntable' argument to use instead of FPKMs but would really appreciate any help in how to start. ...
written 7 days ago by rnaseql0
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Comment: C: TPM from StringTie
... Hi, I would also be interested in the same (but actually at the transcript level). Is there a convenient way to extract all the TPM values for all transcripts for all samples to feed in to Ballgown DE analysis? Thank you very much. ...
written 7 days ago by rnaseql0
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Comment: C: Isoform level differential expression
... Thanks very much for your reply! Indeed, as I am working on hg38, the genome is already very well annotated and while not much may be gained, my project involves in fact trying to assemble de novo (non coding) transcripts so I may still carry on but I really appreciate your suggestions. ...
written 9 days ago by rnaseql0
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Isoform level differential expression
... Hi all, Apologies for double-posting or for perhaps any mistakes in my knowledge but I have been reading around the forums and papers regarding differential expression at the isoform level and am beginning to be quite confused. I have followed the below tutorial for reference guided transcript asse ...
stringtie ballgown rna-seq written 9 days ago by rnaseql0

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