Question: Estimating the abundance of the transcripts and genes using stringtie
gravatar for amy16
17 months ago by
amy1640 wrote:

Hi, Given that the genes and isoforms present in one sample are rarely identical to those present in all other samples in a given experiment, and so they need to be assembled in a consistent manner so that they can be compared, so we merge these GTF files into one single file. When merging is it advised to combine them irrespective of the treatments or group them at this stage itself into control and treatment??

Does the estimation of transcript and gene abundance be performed with respect to the merged file or with respect to the reference gene annotation file??


rna-seq stringtie • 726 views
ADD COMMENTlink modified 9 months ago by iraia.munoa60 • written 17 months ago by amy1640
gravatar for Devon Ryan
17 months ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

Group all of your samples together, regardless of treatment group. That gives you a comparable set of genes/transcripts for quantification.

ADD COMMENTlink written 17 months ago by Devon Ryan90k

Thanks for your valuable suggestion. Very helpful for a beginner like me in this aspect to improve my understanding.

ADD REPLYlink modified 17 months ago • written 17 months ago by amy1640
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