TopHat file.bam file.bed join

Trudy · 04-01-2011, 05:44 AM

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

AlexReynolds · 05-21-2013, 12:59 PM

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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04-01-2011, 05:44 AM	#1
Trudy Member Location: Italy Join Date: Feb 2011 Posts: 16	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

05-21-2013, 12:59 PM	#2
AlexReynolds Member 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.