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Old 04-01-2011, 04:44 AM   #1
Trudy
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Location: Italy

Join Date: Feb 2011
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Default TopHat file.bam file.bed join

Hi all,

I have a question about TopHat alignment.

I have 4 sample alignments and I want to join all together in a only 1 file alignment because these sample belong to the same population (same cellular population but different samples).
I want to join different TopHat output files, so I want to join these information ONLY after individual alignments..

How Can I join the different file.bam and file.bed??? Is it possible??

Thanks in advance
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Old 05-21-2013, 11:59 AM   #2
AlexReynolds
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BEDOPS bam2bed converts BAM to BED. BEDOPS bedops --everything performs a multiset union of BED files.

As an example of how to use them together:

$ bam2bed < myFirstDataset.bam > myFirstDataset.bed
$ bam2bed < mySecondDataset.bam > mySecondDataset.bed
...
$ bedops --everything myFirstDataset.bed ... myLastDataset.bed > myUnionedDataset.bed


The file myUnionedDataset.bed contains reads from all your BAM files, in BED format.
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