How to specify frag len mean and frag len std dev while running cufflinks?
How to specify frag len mean and frag len std dev. My doubt is cufflinks provides mean and std deviation values but we were defining different values. How it is working and is there any other way to specify these values
(cufflinks -p 8 -o HBR_Rep1_ERCC-Mix2 --library-type fr-firststrand --GTF $RNA_HOME/refs/hg19/genes/genes_chr22_ERCC92.gtf --frag-len-mean 262 --frag-len-std-dev 80 --no-update-check $RNA_HOME/alignments/tophat/HBR_Rep1_ERCC-Mix2/accepted_hits.bam )
cufflinks Result: Estimated Mean: 172.02 Estimated Std Dev: 44.21
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