I want to do alignment of paired end fastQ files (R1 and R2) for which I am using BWA MEM tool. As this aligner takes some time to do alignment with single huge fastQ file I split R1 and R2 fastq files in multiple small fastq files(All files followed same sequence of reads as in Original file) and tried to align separately small R1 and R2 pairs. Later on I merged the small SAM files generated and compared the SAM file with SAM file generated with original(huge) fastq files (with picard "CompareSAMs" command). I noticed that the SAM files differ by significant number of reads.
Can anybody please let me know if I am doing it in right way or should I stick to the original files only?
If differences are expected then what might be the possible reason?
Any help on this is really appreciated.