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Old 01-03-2012, 10:14 AM   #1
nguyendofx
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Default Combine PE and SE raw data

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
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Old 01-03-2012, 10:35 AM   #2
adaptivegenome
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1. Map SE data and produce SAM/BAM.
2. Map PE data and produce SAM/BAM.
3. Merge the two BAMs together and sort.
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Old 01-03-2012, 10:50 AM   #3
nguyendofx
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Thanks for promptly response genericforms. merge the BAMs file works great.
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Old 01-03-2012, 10:51 AM   #4
adaptivegenome
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Quote:
Originally Posted by nguyendofx View Post
Thanks for promptly response genericforms. merge the BAMs file works great.
No problem. Good luck.
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