Question: Mapping reads to nuclear, chloroplast, and mitochondria genome separately but all resulting bam files are similar sizes
0
gravatar for kristina.mahan
29 days ago by
kristina.mahan50 wrote:

I mapped reads onto a nuclear, chloroplast, and mitochondrial genome separately using bwa mem and then sorted using samtools. Entire genome: 179 Mb, chloroplast: 169Kb, mitochondria: 43Kb. The resulting bam files are all similar in sizes (23G, 27G, and 27G). Is their an error? Why would this be the case?

ADD COMMENTlink written 29 days ago by kristina.mahan50
3
gravatar for ATpoint
29 days ago by
ATpoint28k
Germany
ATpoint28k wrote:

Because a BAM contains all reads (mapped and unmapped) that were in the original fastq file, so this is normal and expected.

ADD COMMENTlink written 29 days ago by ATpoint28k

so for further process just remove unmapped reads from those bam files?

ADD REPLYlink written 29 days ago by kristina.mahan50

Technically you can do that to reduce file size. If you want that is on you.

ADD REPLYlink modified 29 days ago • written 29 days ago by ATpoint28k

This would be dependent on aligner options. Some aligners will allow you to drop unmapped reads.

ADD REPLYlink written 29 days ago by genomax76k
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