Sequencing center returns data in several files 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?
Usually, a single sequencing library is created from each sample. Assuming you are using barcoded indexes to identify multiple samples, the index is attached to each library, and the libraries are pooled to make a library pool.  A library pool can be frozen, and is very stable.  

A pool can be sequenced multiple times by pipetting a portion of the pool and supplying it to the sequencing process.  Each time, a sample of the molecules in the pool will be sequenced.

Generally, it is true that sequencing runs are very repeatable, and that you will not suffer any batch effects.

If you want to check for batch effects you would need to analyse all of your sequence files separately, and check this first, or in parallel, to your main analysis.

One thing you might want to check is whether the same library pool was sequenced multiple times, or whether separate pools or libraries were made for each sequencing run.  In the second case, there may be more likely to be batch effects.