In bedTools 2.20 if I run:
output.bam.hist.txt
Now in bedTools 2.25 since I can not use -hist and -d together (ERROR: -counts, -d, -mean, and -hist are all mutually exclusive options), I run:
output.bam.hist.txt
The two outputs look very different and basically all that I am trying to get is the depth per nucleotide in the target.bed.
target.bed
Thank you .
Code:
coverageBed -hist -d -abam /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam -b /home/cmccabe/Desktop/NGS/bed/sorted_unix_5column_xgen_targets.bed > /home/cmccabe/Desktop/NGS/pool_I_090215/output.bam.hist.txt
Code:
chr11 1785011 1785099 chr11:1785011-1785099 CTSD 1 17 chr11 1785011 1785099 chr11:1785011-1785099 CTSD 2 20 chr11 1785011 1785099 chr11:1785011-1785099 CTSD 3 20
Code:
coverageBed -hist -abam /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_newheader.bam -b /home/cmccabe/Desktop/NGS/bed/sorted_unix_5column_xgen_targets.bed > /home/cmccabe/Desktop/NGS/pool_I_090215/output.bam.hist.txt
Code:
chr1 14251 14393 X28LU:04862:12482 0 + 14251 14393 0,0,0 1 142, 0, 0 142 142 1.0000000 chr1 16224 16400 X28LU:08504:06628 0 - 16224 16400 0,0,0 1 176, 0, 0 176 176 1.0000000 chr1 16324 16500 X28LU:06201:09146 3 - 16324 16500 0,0,0 1 176, 0, 0 176 176 1.0000000
target.bed
Code:
chr1 955542 955763 + AGRN:exon.1 chr1 957570 957852 + AGRN:exon.2 chr1 976034 976270 + AGRN:exon.2;AGRN:exon.3;AGRN:exon.4
Comment