Problem In Converting Bam To Bed

Question

[camelbbs]

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/

Thanks a lot!

[Istvan Albert]

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.

Answer 1

[Alex Reynolds]

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.

[camelbbs]

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

[Alex Reynolds]

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

[camelbbs]

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

[Alex Reynolds]

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.