The BAM file is sorted using: samtools sort KAPA.bam KAPA.sorted The
When using the -sorted option with files whose chromosomes are not lexicographically
WARNING: File left.bed has inconsistent naming convention for record:
check that the order of the chromosome names and the order of your sort is the same as in the genome. ADD REPLY • link modified 13 months ...
Support fetching all regions from a chromosome (#201, thanks Matt Stone) ... use bedSort to ensure the sort order matches that expected by UCSC tools (# 178)
The merge tool requires that the input file is sorted by chromosome, then by start ... one can also merge intervals that do not overlap, yet are close to one another.
chrom (required) – string naming the chromosome or other contig; start
The chromosome arms dominated by protein-coding genes show enrichment for LMCs.
genomebiology.biomedcentral.com
We denote these as medium-methylated Cs (MMCs) in order to
containing the compiled R code, evaluating to a Pairs object with the closest hits from a and b.