Dear aa,
I am using express to calculate the fpkm after aligning my RNAseq paired ends reads on a transcriptome with bwa. After mapping I got around 42 millions reads mapped (mapped in proper pair). However, after running express in the file results.xprs I obtain around 20 millions total counts (the sum of values in column tot_counts).
I can not understand where the missing 22 millions alignment are? Why were not included in the express output file
Thanks a lot for your support
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