Advice on combining PE125 and PE75 data

[LacquerHead]

Hi all,

Have two experiments, one run on HiSeq PE125 and the other on NextSeq PE75, same V4 chemistry for both. I have thus far chopped 49bp off the PE125 output to get the same 76bp data as from NextSeq to combine replicates. It seems to be ok in terms of downstream peak calling etc, wondering everyones thoughts on whether this is kosher and if so is there a best approach? Thanks!

[mrandel]

I have successfully combined reads from multiple sequencing runs on different Nextera instruments with no problems, as long as the quality scores are reported in the same way.

[LacquerHead]

I guess my central question is whether its ok to combine mapped reads as replicates when they come from PE125 and PE75? In terms of coverage etc etc? Or is my modification of the 125 to 75 appropriate?
Thanks.

I have successfully combined reads from multiple sequencing runs on different Nextera instruments with no problems, as long as the quality scores are reported in the same way.

[Dario1984]

Trimming is the best way to make the datasets comparable.