Hi all, I am having a very hard time completing the tutorial “Essential genes detection with Transposon insertion sequencing” with my own data. I noticed that in the tutorial, all of the DNA sequences (after multiple initial cutadapt invocations) end in the bases ‘TA’ Is this necessary for the analysis so they can be matched to TA sites in the genome? If the processed reads from my own genome do not end in TA is that a problem?
Also, the transposon our lab used was extracted from a plasmid. I have had to eliminate over 75% of reads because their sequences is an exact match to the sequence in this plasmid that immediately follows the MmeI recognition site. Is this a common problem with Transposon sequencing or does it indicate a problem with library prep?