[bvk]

You only have 2 samples anyway. Any sort of metric you'd get from each of the subfiles isn't terribly meaningful unless you're interested in looking at technical variance.

Ok will see. thanks !! But I would like to know like how to check the expression levels of each sample if I run this with merged bam file

[bvk]

Technically cuffdiff command as outlined above will work. But Devon has already warned you about the consequence in post #5.

Yes, I agree but I would like to know how to check the expression levels of each sample if I run this with merged bam file.

[bvk]

Technically cuffdiff command as outlined above will work. But Devon has already warned you about the consequence in post #5.

I used this in command line:

cuffdiff -o diff_out4 -b ../genome/ce10.fa -p 2 -L larval,early -u merged_asm/merged.gtf ../tophat/em/SRR493359_60_61_thout/accepted_hits.bam ../tophat/em/SRR493363_64_65_thout/accepted_hits.bam

Now I want to run this from a python script. So, I gave a call in this way.

do.call([cfg.tool_cmd("cuffdiff"), "-p", str(cfg.project["analysis"]["threads"]), "-b", str(cfg.project["genome"]["fasta"]), "-u", cfg.project["samples"][0]["files"]["merging_gtf"], "-L", str(cfg.project["phenotype"][0]), str(cfg.project["phenotype"][1]), "-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])

but I get an error: invalid syntax. Can you please help in this?