Combine PE and SE raw data

[nguyendofx]

Hi All,

I have a pair-end and single-end data from two difference illumina runs (the same biological sample). What are the best way to combine both data sets for downstream analysis?

1. Combine FASTQ/QSEQ from both run, then align with a aligner?

2. Align each individual data set, then combine BAMs file together?

Thanks,
Ng

[adaptivegenome]

1. Map SE data and produce SAM/BAM.
2. Map PE data and produce SAM/BAM.
3. Merge the two BAMs together and sort.

[nguyendofx]

Thanks for promptly response genericforms. merge the BAMs file works great.

[adaptivegenome]

Thanks for promptly response genericforms. merge the BAMs file works great.

No problem. Good luck.