Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: MSA program that allows collpase of identical reads
0
gravatar for blur
5 months ago by
blur • 150
European Union
blur • 150 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,
collapse msa multi sequence alignmen • 151 views
ADD COMMENT • link •
modified 5 months ago by Mensur Dlakic • 8.3k • written 5 months ago by blur • 150

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

ADD REPLY • link written 5 months ago by blur • 150
0
gravatar for Mensur Dlakic
5 months ago by
Mensur Dlakic • 8.3k
USA
Mensur Dlakic • 8.3k wrote:

You don't need to create an MSA in order to achieve this. Dedupe in BBmap does exactly what you want.
ADD COMMENT • link written 5 months ago by Mensur Dlakic • 8.3k

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 REPLY • link written 5 months ago by blur • 150
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1059 users visited in the last hour
_