Dear all,
when i use cuffcompare to combine the cufflinks output for 2 samples, i found that the output prefix.loci file has totally different number of combined loci when using or not using -r parameter.
when using -r as follows, prefix.loci has 3814 loci
when not using -r as follows, prefix.loci has 6339 loci
In my opinion, I think the -r option is only used to compare rna-seq data to the reference annotation. Why the number of output loci can be dramatically affected by the -r parameter?
when i use cuffcompare to combine the cufflinks output for 2 samples, i found that the output prefix.loci file has totally different number of combined loci when using or not using -r parameter.
when using -r as follows, prefix.loci has 3814 loci
cuffcompare -o cuffcompare_output -s ~/rd/ucsc_resource/genome/hg19/by_chr/ ../cufflinks/BN189637/transcripts.gtf ../cufflinks/BT189637/transcripts.gtf -r Ens_Reformat_Homo_sapiens.GRCh37.60.gtf
cuffcompare -o cuffcompare_output -s ~/rd/ucsc_resource/genome/hg19/by_chr/ ../../cufflinks/BN189637/transcripts.gtf ../../cufflinks/BT189637/transcripts.gtf
