DE analysis with a genome guided approach

[Kishor Kumar Sarker]

Hi,
I Hope everyone is doing well. I want to do a DE analysis with a
genome guided approach. I have found the cmdline for individual genome
guided assembly. But cmdline for genome guided assembly using
replicates from different individuals is yet to be found. Can someone
please guide me？

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With best regards,

Kishor Kumar Sarker

(PhD Researcher)
Lab of Molecular Systematics and Ecology
Faculty of Life Sciences
Shanghai Ocean University, Shanghai, China
Phone: +8618621974360

[Brian Haas]

Hi Kishor,

For genome guided assembly with multiple replicates, just first merge the bams into a single genome aligned bam file (samtools merge should work).  Then use that single bam for the assembly.

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Kishor Kumar Sarker]

Hi,
Does that mean if I have 20 replicates from two treatments, I would need to make 20 individual alignments against the genome, and then I need to start the assembly from a merged bam file?

[Brian Haas]

Yes, align then merge then assemble.

best,

Brian

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