How to obtain unique reads on Galaxy

Question

[miriam115]

Hi,

I am trying to use Galaxy for some NGS data. I aligned the data by using bowtie2. I can't figure out how to extract only the unique-mapped reads.

On the report of the alignment I can see this message:

"20552525 (13.02%) aligned 0 times

83720562 (53.02%) aligned exactly 1 time

53619781 (33.96%) aligned >1 times".

And I want only the 53.02%.

I am looking for any sort of help - on Galaxy.

Thanks

[Joseph Pearson]

On Galaxy, both BAMtools (NGS:BAMtools and SAMtools (NGS:SAMtools) can filter on the bit flags. It looks like the BAMtools filter set is a little more intuitive. I think if you play with the combinations of filters, you should be able to get your 53.02%.