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Problem In Converting Bam To Bed

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!

format seq
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updated by Alex Reynolds Alex Reynolds • written by camelbbs camelbbs

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.

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written by Istvan Albert Istvan Albert

1 answer

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.

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written by Alex Reynolds Alex Reynolds

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

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written by camelbbs camelbbs

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

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written by Alex Reynolds Alex Reynolds

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

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written by camelbbs camelbbs

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.

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written by Alex Reynolds Alex Reynolds

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