Hi all
We've got a few RNA-Seq experiments planned running multiplexed samples, such that all samples to be analysed are run in a single library. Because of the high number of samples involved (30-60), we are running several lanes to make up the sequencing depth.
So prior to carrying out differential gene expression analyses, I would have to merge data for the same sample across the different lanes (e.g. for Sample A in lanes 1,2 and 3: A1 + A2 + A3).
When would be the appropriate time to merge the data?
Should I merge the aligned bams of A1,A2,A3 and then count reads in genes e.g. with HTSeq-count?
Or should I count A1, A2 and A3 separately then add up the counts for all the genes across lanes?
Does anyone have any experience or opinions on this?
We've got a few RNA-Seq experiments planned running multiplexed samples, such that all samples to be analysed are run in a single library. Because of the high number of samples involved (30-60), we are running several lanes to make up the sequencing depth.
So prior to carrying out differential gene expression analyses, I would have to merge data for the same sample across the different lanes (e.g. for Sample A in lanes 1,2 and 3: A1 + A2 + A3).
When would be the appropriate time to merge the data?
Should I merge the aligned bams of A1,A2,A3 and then count reads in genes e.g. with HTSeq-count?
Or should I count A1, A2 and A3 separately then add up the counts for all the genes across lanes?
Does anyone have any experience or opinions on this?
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