How to concatenate bed files before flair collapse

[chenxing-zhang]

I run flair-correct for each samples and then obtain corrected.bed for each samples. Before i run flair-collapse, i notice that "If there are multiple samples to be compared, the flair-corrected read bed files should be concatenated prior to running flair-collapse." How to concatenate bed files before flair collapse?

[diekhans]

BEDs are line-orient files, you can use the cat command.

chenxing-zhang @.***> writes:

I run flair-correct for each samples and then obtain corrected.bed for each samples. Before i run flair-collapse, i notice that "If there are multiple samples to be compared, the flair-corrected read bed files should be concatenated prior to running flair-collapse." How to concatenate bed files before flair collapse?

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[chenxing-zhang]

Thanks. The following code is what I used, share it with others:

cat <list of corrected.bed>| sort -k1,1 -k2,2n -k3,3n > concatenated_corrected.bed