I am new on this forum, and on genome sequencing/assemblies/ first analyses of a genome so I will ask for your indulgence! I have received a new eukaryote genome, and I have some difficulties to understand to what correspond each file I have!
Particularly it seems that I have one range of files corresponding to a HiSeq sequencing: For which I have a forward and a reverse file, and for each of them I have a PE and a SE file. These files are under a folder named "cleaned", when I also have a folder named raw, containing only two files, a forward and a reverse. I would guess it is the "Pair end" and "single end", but in this case, I don't understand why I have both reverse and forward for the Single end sequencing? I might completely misunderstood what are my data then...
I also have the same type of files for what seems to correspond to a MiSeq sequencing.
Besides, I also have two folders containing LJD, for Long Jumping Distance files (processed and processed_cleaned) And I have 2 ranges of files in them: some "3kb" and "8kb" and for each of them, a forward, a reverse and a singleton. I am not sure to understand if LJD is another way of HiSeq sequencing providing longer reads or type of assembly. And in any case, I don't understand what is the difference between 3kb and 8kb. Are these different files supposed to be used together or are they different treatment of the same obtained sequences
I am completely aware that my questions maybe very naive, so I will be grateful for any help! Thank you in advance!!