union of two sequencing fastq files

[paolo.kunder]

Dear All,

I just received some MeDIP sequencing data.
Out of 4 samples, one is really low in total reads number.
Due to this the service will provide me some additional reads (resequencing the sample) to compensate this difference.

A naive question, is it correct to merge the two fastq files, or I better merge the sam files? or is the same?

Thanks,
Paolo

[dpryan]

There's no practical difference between merging the fastq files or merging the SAM files. One could argue that if these are paired-end reads, then the SAM files should be merged in case you use an aligner that re-estimates insert size (this could be different if the second sequence batch comes from a different library prep), but that's not terribly likely to create a big issue.