bam file to .bedgraph
4
0
Entering edit mode
6.1 years ago

I have bam files and i need to convert them to .bedgraph format for my further analysis please help me in this issue?

RNA-Seq ChIP-Seq Galaxy R genome • 14k views
ADD COMMENT
5
Entering edit mode
6.1 years ago

Your questions is lacking a couple of details such as what's the goal of obtaining the bedGraph file, do you want to normalize or scale the read counts, do you want the read counts for the entire genome, what type of data is this, have you tried any tools and found them lacking some options, ....

To answer your general question in a general manner: bedtools genomecov with -bg option or deepTools bamCoverage might be viable options.

ADD COMMENT
1
Entering edit mode

If you want per-million scaled bg, use this command together with genomecov:

## Scaling factor for single-end data, counting every mapped read (bitwise flag = 0)
 TmpScale=$(bc <<< "scale=6;1000000/$(samtools view -f 0 -c in.bam)")

 ## Now get the actual bedGraph:
 echo '==> RPM scaling factor:' $TmpScale
 bedtools genomecov -bga -ibam in.bam -scale $TmpScale | sort -k1,1 -k2,2n > out.bedGraph
ADD REPLY
0
Entering edit mode

To answer your general question in a general manner

The question was quite specific.

ADD REPLY
2
Entering edit mode
6.1 years ago
trausch ★ 1.9k

Alfred is another option:

alfred tracks -o out.bedGraph.gz input.bam
ADD COMMENT
1
Entering edit mode
6.1 years ago

BEDOPS bam2bed can be useful:

$ bam2bed < reads.bam | cut -f1-3,5 > reads.bg

This puts the map quality signal into the fourth column of reads.bg. Other columns are available: http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/bam2bed.html

If you're trying to count reads over regions, you could instead do something like:

$ bedmap --echo-ref-name --count --delim '\t' regions.bed <(bam2bed < reads.bam) | sed 's/[:-]/\t/g' > answer.bg
ADD COMMENT
1
Entering edit mode
6.1 years ago

This can be done using bedtools genomecov or genomeCoverageBed .

bedtools genomecov [OPTIONS] -ibam < input file name> -g <genome> -bg <output name>
ADD COMMENT

Login before adding your answer.

Traffic: 1232 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6