Question: Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis
gravatar for amy16
14 months ago by
amy1640 wrote:

Hi all, I am using Stringtie for transcript assembly and quantification. My experimental design includes 4 different genotypes each under two treatment conditions with sim to identify differential gene expression analysis. I did the sequence alignment to the reference genome and the used Stringtie to assemble the transcripts. I am not clear about the --merge function in stringtie. Which GTF files should I use to merge the transcripts?? After running the initial stringtie function for transcript assembly, there are these following output files, B1C_transout.gtf and B1C_cov_refs.gtf for each sample. Do I merge these two GTF files?? And then estimate the expression values to generate the CTAB files??


ADD COMMENTlink written 14 months ago by amy1640

StringTie's merge function

ADD REPLYlink written 14 months ago by genomax63k

Thanks for directing me!!!!

ADD REPLYlink written 14 months ago by amy1640
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