Per Base Coverage
Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.
• 4,966 views
•
link
updated
by
Aaronquinlan
•
written
by
Info_Nowise •
•
written
by
Info_Nowise •
2 answers
samtools depth your.bam
• 1 views
•
link
updated
by
Ram
•
written
by
Zev.Kronenberg
•
written
by
Zev.Kronenberg
Also,
bedtools coverage -abam aln.bam -b regions.bed -d
• 1 views
•
link
updated
by
Ram
•
written
by
Aaronquinlan
•
written
by
Aaronquinlan
Log in to answer this question.
More posts like this
-
Overlapping reads between two BED windows
written by pablo
-
How to obtain zero-based coordinates read depth using bedtools coverage for a specific region?
written by vladimiralan •
-
What exactly does the -fs flag (fragment size) do in bedtools genomecov/genomeCoverageBed?
written by kieft1bp •
-
Median coverage from BAM file
written by firestar
-
genomeCoverageBed and supplementary alignments
written by giovanni.bacci •
-
genomeCoverageBed for paired end reads
written by Vanilla
-
per bp depth intersected with gff file
written by Biomonika (Noolean)
-
Counting The Whole Insert Size From Paired-End Reads As Coverage
written by Alastair Kerr
-
Samtools Mpileup Options
written by Info_Nowise •
-
Intersecting A Set Of Bam Reads With A Set Of Coordinates
written by User 9996
