Hello,
I received some data from a sequencing facility, that supposedly have always used the Illumina Nextseq 2000 P3 flow cell 50 cycles kit. However in the different batches of sequencing, the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended. Anybody has an idea on why would they do that? That flow cell/kit can even handle more cycles than 50? I am not completely familiar with the wet lab sequencing part.
2 answers
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unless you anticipate having to compare to other samples on a shorter run, in which case, trim the fastqs to match the shortest reads you have
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If they sent data that is not what you requested then you have every reason to talk to them and ask for an explanation/fix.
If you got longer sequences than you requested (and you don't need/want the longer length) then you can simply chop the extra bases off. You would not want to use data that was different length, a mix of single- and paired-end for different samples in a particular experiment.