High no feature counting when using strand specific data
As i'm analyzing strand-specific RNA-seq data, prepared with Epicenter kit, I used HT-Seq count with the option: -s yes Some of my samples had only ~50% counted reads (the rest is had no feature) while others over 85%. i tried to count again, this time -s no, than all of my samples had over 85% counted.
Consulting with the library preparation staff, we checked for DNA presence but couldn't found any abnormal levels.
any idea how to move on or what might be the cause ?
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I have no experience with the epicentre kits, but chances are you need
-s reverse(if this kit uses the dUTP method for strand specificity)