We've just had some RRBS data returned for the first time. I am told by the CRO that it's a non-directional, Msp1 library. My head is swimming from trying to work out the combinations of read pairs etc that might be present, but one thing I thought I was sure of was that all of our reads should have the Msp1 site at the start.
However, the data for the first mate in all our samples does not appear to have the restriction site. The attached image shows the FastQC plot for "per base sequence content" for the first mate of sample 1 (left side) and second mate of sample 1 (right side). I have done nothing to this data - the CRO has adapter trimmed. We see the Msp1 site fragment in the second mate (on the right), but not for the first mate (on the left). I see the same for all the samples in this experiment.
Q1 - am I right, we expect the Msp1 site in ALL reads?
Q2 - if so, whats gone wrong here?
(am awaiting a response from the CRO)
However, the data for the first mate in all our samples does not appear to have the restriction site. The attached image shows the FastQC plot for "per base sequence content" for the first mate of sample 1 (left side) and second mate of sample 1 (right side). I have done nothing to this data - the CRO has adapter trimmed. We see the Msp1 site fragment in the second mate (on the right), but not for the first mate (on the left). I see the same for all the samples in this experiment.
Q1 - am I right, we expect the Msp1 site in ALL reads?
Q2 - if so, whats gone wrong here?
(am awaiting a response from the CRO)
Comment