RRBS (Reduced Representation Bisulfite Sequencing)

Question

[sk_24]

I am working with single-end RRBS data, but I do not have information about the restriction enzyme used during library preparation. Trim Galore offers the --rrbs option, which is tailored for data generated using the MspI enzyme. Is there a way to confirm from my raw FASTQ files whether MspI was used for restriction digestion?

Answer 1

[dthorbur]

You should have enrichment of specific restriction enzyme motifs at the start of your reads. If your reads often start with something like CCGG or CGG, then it's likely MspI.

[ATpoint]

Beyond that, guys, how is it that there is no documentation about your experiments. This can't be. Publication needs an adequate methods text...

[sk_24]

Not my fault

[dthorbur]

Whilst this may be true, I second ATpoint, you should try to not work with collaborators that are this disorganised. If you don't even know the restriction enzyme, how are you going to publish this? All this hard work and potentially interesting results will likely not get past preprint.

[GenoMax]

It is possible that the data is from a public source (e.g. SRA) and thus the details on methodology may be unclear.

[dthorbur]

Fair, I didn't really think of that in the moment. But it's a similar issue, if the methods are so unclear, you can't really be that confident of any results since you can't escape the possibility of an undescribed treatment causing all your nice tidy results.