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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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BED vs BAM #70

Closed gireeshkbogu closed 6 years ago

gireeshkbogu commented 7 years ago

Hi,

How could I run ngsplot on BED format instead of BAM? Ex: chr1 10147 10183 N 1000 - chr1 10159 10195 N 1000 - chr1 10317 10353 N 1000 + chr1 10496 10532 N 1000 +

FYI: All ROADMAP epigenetic data (tagalign) has been stored in BED format. It would greatly useful if there is a way to plot this public data using your tool. thanks http://egg2.wustl.edu/roadmap/data/byFileType/alignments/unconsolidated/H3K4me3/

ny-shao commented 6 years ago

Hi gireeshkbogu,

I would suggest giving bedtobam of bedtools a try: http://bedtools.readthedocs.io/en/latest/content/tools/bedtobam.html Don't forget to set -mpaq to 254 instead of the default 255, as 255 is not a standard validated value in SAM criteria.

Ning-Yi