We send some samples to sequence and we got several (fastq.gz) files for each sample. The files are distributed at two or three folders with different dates (more than a week apart). The dates of the folders where the data is in:
2019-08-12 2019-08-21 2019-08-21 2019-09-04 2019-09-14
I asked the facility about why there are the same file in different folders, and they told us that:
we have split sequencing of that project on different flowcells, so all files are correct and you have to merge the individual (duplicate) files to get the requested total read numbers.
How can different flow cells be from the same experiment and be run with more than a week of difference? (I thought that all the flow cells are run at the same time in each sequencing)
Can be there some batch effect? How can I check if there is batch effect if we merge the files before trimming, mapping and counting?