Question: bam file to .bedgraph
0
gravatar for praveenhcu131
14 months ago by
praveenhcu1310 wrote:

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 • 1.7k views
ADD COMMENTlink modified 14 months ago by arup1.5k • written 14 months ago by praveenhcu1310
3
gravatar for Friederike
14 months ago by
Friederike4.5k
United States
Friederike4.5k wrote:

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 COMMENTlink written 14 months ago by Friederike4.5k

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 REPLYlink written 14 months ago by ATpoint19k
1
gravatar for trausch
14 months ago by
trausch1.3k
Germany
trausch1.3k wrote:

Alfred is another option:

alfred tracks -o out.bedGraph.gz input.bam
ADD COMMENTlink written 14 months ago by trausch1.3k
0
gravatar for Alex Reynolds
14 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

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 COMMENTlink modified 14 months ago • written 14 months ago by Alex Reynolds28k
0
gravatar for arup
14 months ago by
arup1.5k
India
arup1.5k wrote:

This can be done using bedtools genomecov or genomeCoverageBed .

bedtools genomecov [OPTIONS] -ibam < input file name> -g <genome> -bg <output name>
ADD COMMENTlink written 14 months ago by arup1.5k
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