Q. Is my BAM file sorted?
A. Run samtools view -H <file> | grep SO:. If sorted, should indicate the sort order
otherwise say unsorted. Further, the bam index files generated from the
unsorted files are of smaller size (hence look fishy).
Q. Is my data paired-end or single-end sequenced?
A. Run samtools flagstat <file>; should indicate the number of reads in
paired-end mode along with total number of reads.
Q. What are the blacklist regions across species? A. See here: https://sites.google.com/site/anshulkundaje/projects/blacklists
Q.