Question: Problem In Converting Bam To Bed
0
gravatar for camelbbs
7.8 years ago by
camelbbs670
China
camelbbs670 wrote:

Hi, I have a question in converting bam to bed, while convert bam to bed and import them to IGV, you can see they are different. Only bam file can align well to refseq exons. Does bedtools change the genome coordinates in bam files?

image:

http://postimage.org/image/68ynlxui3/

IGV

Thanks a lot!

seq format • 2.3k views
ADD COMMENTlink modified 7.8 years ago by Alex Reynolds30k • written 7.8 years ago by camelbbs670

generate a plot that only shows the bam and the bed file. Make sure to show the bam file and not the coverage of it. Please specify in your post the command that you use to generate the bed file. You can edit your answer and put that information in there.

ADD REPLYlink modified 7.8 years ago • written 7.8 years ago by Istvan Albert ♦♦ 84k
1
gravatar for Alex Reynolds
7.8 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

If you would like to see if the problem is with conversion, we have a bam2bed script available for download. This might be a way to do an independent "sanity check" of sorts.

ADD COMMENTlink written 7.8 years ago by Alex Reynolds30k

My data is RNAseq, can that fit your script? Thanks!

ADD REPLYlink written 7.8 years ago by camelbbs670

Try it out and let us know if it doesn't help.

ADD REPLYlink written 7.8 years ago by Alex Reynolds30k

I want to generate a format that can be viewed in IGV.

ADD REPLYlink modified 7.8 years ago • written 7.8 years ago by camelbbs670

I have to admit I haven't played too much with IGV in a few years. But if IGV imports UCSC BED data, then our script should help translate the BAM data to BED.

ADD REPLYlink written 7.8 years ago by Alex Reynolds30k
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