ENCODE BAM

ENCODE(phase 2) provides RAW files and BAM files for downloading. However, it's always recommended to start from aligning FASTQ RAW files instead of directly using BAMs. The reason is that even from the same lab, BAM files may be generated from different pipeline (e.g., BWA, BOWTIE or ELAND). The BAM headers and certain annotations (e.g., XA tag) may be different across different aligners. Mixing them in downstream analysis will cause unpredictable mistakes!