pData in RNA differential Expression analysis using Ballgown

Question

[GenomicsNewbie]

Hi everyone,

I am doing RNA-seq DE analysis using Ballgown. Here I have a question on pData.

I see that some people use merged BAM files as one sample. For example, let's say I have the following data: Norm_Lane1.bam, Norm_Lane2.bam

Then I would merge them and have Merged_Norm.bam

Using stringtie, I estimate abundance for individual lanes of data, but also for the merged BAM.

In that case, would it be appropriate to use Norm_Lane1.bam, Norm_Lane2.bam, Merged_Norm.bam as my pData in Ballgown? Or should I only use Norm_Lane1.bam, Norm_Lane2.bam

[ATpoint]

Differential transcript or differential gene expression?

[GenomicsNewbie]

I am currently looking at differential gene expression, but would the answer be different?

[ATpoint]

Yes because ballgown is not suited for gene level analysis. Use something like DESeq2 or edgeR.