I had similar problems. I had not bad qualities in the RNA-seq reads but very poor quality in the index reads that turned out in a lot of reads without index assignment during demultiplexing.
Here you can see some images of the cluster density and >30quality boxplots (lane 3,4 and 5 are the RNA-seq single read 50 cycles)
Here you can see some images of the cluster density and >30quality boxplots (lane 3,4 and 5 are the RNA-seq single read 50 cycles)
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