Hi,
We have performed transcription start site sequencing (TSS, 5'-sequencing) using TAP treatment (tap+ and tap- of totalRNA) and Illumina 100bp SE sequencing. I have quality trimmed the reads with Trimmomatic and mapped to the genome using TopHat2. For the tap+ reads, about 50% of the trimmed reads map to the genome, and for tap- only about 20% map.
Have anyone experienced similar results? What could be the reasons for the low overall mapping rate, and why is the tap- data lower than tap+? I don't fully understand what is the effects of the tap-treatments, and what should be the expected differences between the two libraries. We are working on a non-model organism with a quite poorly assembled genome, but with regular mRNA-seq we usually have 80% mapping rate.
We have performed transcription start site sequencing (TSS, 5'-sequencing) using TAP treatment (tap+ and tap- of totalRNA) and Illumina 100bp SE sequencing. I have quality trimmed the reads with Trimmomatic and mapped to the genome using TopHat2. For the tap+ reads, about 50% of the trimmed reads map to the genome, and for tap- only about 20% map.
Have anyone experienced similar results? What could be the reasons for the low overall mapping rate, and why is the tap- data lower than tap+? I don't fully understand what is the effects of the tap-treatments, and what should be the expected differences between the two libraries. We are working on a non-model organism with a quite poorly assembled genome, but with regular mRNA-seq we usually have 80% mapping rate.
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