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Old 05-09-2016, 05:11 AM   #1
Sbamo
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Location: Germany

Join Date: Jan 2016
Posts: 7
Default Should discordant pairs be used for counting/DGE?

Hello everyone,

I am using the STAR aligner, which reports discordant pair alignments in a seperate BAM file. Using my workflow I want to search for differentially expressed genes, transcripts and exons.

My question:
- Should I calculate feature counts using only the concordant pairs or include the discordant pairs for counting?

Note that I am examining samples for patients with leukaemia, where gene fusions are common events and have been detected in my samples using other methods. There are around 100000-500000 pairs (out of ~30 million) reported as discordantly aligned.

I am afraid that including discordant pairs will introduce a bias in calculating gene expression. Excluding them, on the other hand, could also introduce a bias. Any and all ideas are welcome! Thanks!
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