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Old 04-01-2011, 05:44 AM   #1
Location: Italy

Join Date: Feb 2011
Posts: 16
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
Trudy is offline   Reply With Quote
Old 05-21-2013, 12:59 PM   #2
Location: Seattle, WA

Join Date: Feb 2013
Posts: 45

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.
AlexReynolds is offline   Reply With Quote

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