Question: MSA program that allows collpase of identical reads
0
gravatar for blur
5 months ago by
blur150
European Union
blur150 wrote:

Hi,

I want to create an MSA and then collapse the identical reads, so that I can see the different TYPES of reads in my MSA. Any ideas what program allows such options?

Thanks,

ADD COMMENTlink modified 5 months ago by Mensur Dlakic8.3k • written 5 months ago by blur150

I found a way - I used the fastx program http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_collapser_usage

ADD REPLYlink written 5 months ago by blur150
0
gravatar for Mensur Dlakic
5 months ago by
Mensur Dlakic8.3k
USA
Mensur Dlakic8.3k wrote:

You don't need to create an MSA in order to achieve this. Dedupe in BBmap does exactly what you want.

ADD COMMENTlink written 5 months ago by Mensur Dlakic8.3k

This seems close to what I need - but I also need to be able to count the no. of duplicates per type and I can't seem to find this option in the manual... The endpoint is to count the number of each as per the total reads available.

ADD REPLYlink written 5 months ago by blur150
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