I found that in the ENCODE database, hg19 v19 contain two bam files for each biological replicate, and they are different bam file, so what is the difference between the two bam file?
Here is an example: https://www.encodeproject.org/experiments/ENCSR109IQO/ Both ENCFF353VRV and ENCFF042VVP belong the hg19 alignment biological replicate 2.
1 answer
As indicated on the page you linked they are isogenic replicates. Here is the definition from ENCODE project.
Isogenic replication - Biological replication. Two replicates from biosamples derived from the same human donor or model organism strain. These biosamples have been treated separately (i.e. two growths, two separate knockdowns, or two different excisions).
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