bamtobed (naive) question

[proux]

Apologies in advance...

I am using samtools bamToBed in my mac el capitan terminal.

I get what looks to be the appropriate output in all chromosomes after some time.

How do I actually save this as a .bed file? Or, if it is autosaved, where do I find it?

[mastal]

What was the command that you used to create the bedfile?

I expect that it should be either in your working directory - the directory that you called the command from, or the directory where your bam file is, and should have the same name as your bam file, but with the suffix .bed.

[proux]

Thanks, I thought so boy couldn't find it, will look harder tomorrow

I used bamtobed -i <file.bam>

[WhatsOEver]

If you use the command as it is, you get everything printed in your terminal, don't you?
So, you simply have to redirect in into a file: "bamToBed -i yourBamFile.bam > ./SaveItInTheCurrentFolder.bed

[proux]

If you use the command as it is, you get everything printed in your terminal, don't you?
So, you simply have to redirect in into a file: "bamToBed -i yourBamFile.bam > ./SaveItInTheCurrentFolder.bed

exactly! I worked it out eventually, thanks!