wheter combine FASTq or bam files after alignment

[honey]

I have some Hi-seq data from three samples. The underlying principal of experiment is there is an infection of bacteria and I am intrested in studying DE of human as well as bacterial genes. I have succesfully performed analysis on human genome, however for bacterial anlaysis - I wonder should I first combine two FASTq file (two replicates of SE) and then perform alignment or should it be ok to align these replicates seprately and then combine bam file.
Thr reason this question is bothering me as by mistake wet lab ran the same sample in two different lanes. I was thinking since chances of amount of bacterial genome will be very small I may loose important information if I align them seprately.
Any suggestion?
Thanks.

[westerman]

Same sample but two different FastQ files? I would merge the two FastQ files first and then do the alignment.

[aangs94]

I have some Hi-seq data from three samples. The underlying principal of experiment is there is an infection of bacteria and I am intrested in studying DE of human as well as bacterial genes. I have succesfully performed analysis on human genome, however for bacterial anlaysis - I wonder should I first combine two FASTq file (two replicates of SE) and then perform alignment or should it be ok to align these replicates seprately and then combine bam file.
Thr reason this question is bothering me as by mistake wet lab ran the same sample in two different lanes. I was thinking since chances of amount of bacterial genome will be very small I may loose important information if I align them seprately.
Any suggestion?
Thanks.

Hello Honey,

Since the date of your question about combining files, did you find any additional answers?
I am asking me the same question

Thanks very much.