Hi everyone. So I have another doubt about processing reads for miRNA-seq.
In the parameters I've recieved from the lab doing the sequencing process, they specify this:
5 ́AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTGGGA3 ́
5 ́CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT3 ́
Also they specify a series of short index sequences for each sample, as follows:
ID Index Sequence 7005 ATCACG 7006 CGATGT 7007 TTAGGC . . .
I don't know what specific protocol they used to make the libraries, but I assume that what specified in Index primers is what I should trimm from my reads, being them in the NNNN fragment included between both primers to trim. But, what do the Index Sequence refer to? And what about the Sequence Reference primer (SR primer)? I don't know if I should also include them in a list of sequences to trim or not...
Any help to put some light in this?