While processing Illumnia paired-end reads, dataset of mine gave rise to both - paired-end and single-end due to read filtering based on phred score. Is there any way to map both dataset into the reference genome to generate single sam file using bwa aligner?
Hi,
I am not sure if you need to map everything at the same time, but if the goal is to obtain a single sam/bam file you can:
1) Map independently both datasets with bwa or other mapping tool.
2) Convert the sam files to bam files with samtools view -Sb -o file.bam file.sam
3) Merge bam files with samtools merge out.bam bam1 bam2
(more info about samtools: http://samtools.sourceforge.net/samtools.shtml)
Good luck,
To the best of my knowledge, you can just provide the files as paired or unpaired. You can always merge the SAM files later.
Wish you a very happy new year, 2013.
Thank you everyone for your answers.
Your answer helped me a lot to understand the topic. I hope what Dr. Aureliano Bombarely suggested, will meet my criteria perfectly. And will get back to you after geting he result.
You may need the single end and pair end data in separate ways.
It help the downstream analysis after initial mapping.
e.g)
single-end + pair-end => variant calling
pair-end => structural variation, copy number variation
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