How to work with biological replicates
Hello everyone,
I am working with small-RNA(~50ntds) cancer samples, RNA-seq data. I have tumors and normal cell samples with biological replicates of each sample. Using bed-tools coverageBed I counted the read distribution in genomic regions as well as in 10kb interval chr regions and identified the correlation. My problems are:
-All my biological replicates are showing good correlation except one (good ones=0.98,0.96 etc bad one =~0.6) so now I want to know the methods to study for correlation of biological replicates.
-How can I compare and extract meaningful regions from the above badly correlated replicate.
-Can anybody tell the correct method for identifying correlation and coverage depths of biological replicates?
Please help & tell me how should I proceed.
Thanks.
I am working with small-RNA(~50ntds) cancer samples, RNA-seq data. I have tumors and normal cell samples with biological replicates of each sample. Using bed-tools coverageBed I counted the read distribution in genomic regions as well as in 10kb interval chr regions and identified the correlation. My problems are:
-All my biological replicates are showing good correlation except one (good ones=0.98,0.96 etc bad one =~0.6) so now I want to know the methods to study for correlation of biological replicates.
-How can I compare and extract meaningful regions from the above badly correlated replicate.
-Can anybody tell the correct method for identifying correlation and coverage depths of biological replicates?
Please help & tell me how should I proceed.
Thanks.