difference between data sets in alignment rate

Question

[zizigolu]

Hi,

I have a question.

I used the same reference for genome building and alignment with bowtie2 but I really can't get why the rate of alignment for different data sets (experiments) are pretty different. for example alignment rate in GSE63789 and GSE67387 are too low and high respectively but the process I did are the same and both are Illumina.

Thank you for any guidance

Answer 1

[harold.smith.tarheel]

Differences in the amount of ribosomal RNA contamination are the most common explanation for dramatically different mapping rates in RNA-Seq.