Hello,
My input files are:
Here's a sample of regions.bed
The objective is to obtain which intervals of "regions.bed" design are not being covered in bam.
I think my problem is that i need to generate a BED file from the original BAM representing the regions that are being covered. And I've no idea how to do that.
I've tried converting the bam input into a bed file with bedtools. Then intersecting both bed files with -v option with bedtools intersect.
The problem comes when I get this weird output in resulting bed file:
That 0 value is really weird...
chr1 10833 10931 M01167:3:000000000-A37T8:1:1110:11018:11790/1 0 + 10833 10931 0,0,0 1 98, 0,
chr1 10977 11027 M01167:3:000000000-A37T8:1:1101:10241:4209/2 0 + 10977 11027 0,0,0 1 50, 0,
And lines being repeated even if it's not the same read:
chr1 10292578 10292679 M01167:3:000000000-A37T8:1:2104:17089:16810/1 60 - 10292578 10292679 0,0,0 1 101, 0,
chr1 10292579 10292680 M01167:3:000000000-A37T8:1:2105:8403:22087/1 60 - 10292579 10292680 0,0,0 1 101, 0,
chr1 10292579 10292680 M01167:3:000000000-A37T8:1:2112:16677:2861/1 60 - 10292579 10292680 0,0,0 1 101, 0,
Thank you.
Best regards,
gmarco.
My input files are:
- input.bam (paired end) Illumina alignment obtained with BWA.
- regions.bed file which contains the intervals of the current design
Here's a sample of regions.bed
Code:
chr1 10292367 10292512 chr1 10316285 10316401 chr1 10318531 10318750 chr1 10321943 10322048 chr1 10327418 10327636 chr1 10328190 10328341
I think my problem is that i need to generate a BED file from the original BAM representing the regions that are being covered. And I've no idea how to do that.
I've tried converting the bam input into a bed file with bedtools. Then intersecting both bed files with -v option with bedtools intersect.
The problem comes when I get this weird output in resulting bed file:
That 0 value is really weird...
chr1 10833 10931 M01167:3:000000000-A37T8:1:1110:11018:11790/1 0 + 10833 10931 0,0,0 1 98, 0,
chr1 10977 11027 M01167:3:000000000-A37T8:1:1101:10241:4209/2 0 + 10977 11027 0,0,0 1 50, 0,
And lines being repeated even if it's not the same read:
chr1 10292578 10292679 M01167:3:000000000-A37T8:1:2104:17089:16810/1 60 - 10292578 10292679 0,0,0 1 101, 0,
chr1 10292579 10292680 M01167:3:000000000-A37T8:1:2105:8403:22087/1 60 - 10292579 10292680 0,0,0 1 101, 0,
chr1 10292579 10292680 M01167:3:000000000-A37T8:1:2112:16677:2861/1 60 - 10292579 10292680 0,0,0 1 101, 0,
Thank you.
Best regards,
gmarco.
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