extract multiples regions from IGV

Question

[Morris_Chair]

Hello Everyone,

From my ChIP-seq picks.file, I selected regions from where I want to see if there is any consensus sequence. Is there a way to extract all this nucleotide sequences (about 300) from IGV ? or is there any other tool to do that ?

Thank you :)

[GenoMax]

From IGV or BAM? Do you want sequence from BAM or screenshots from IGV for regions you are interested in?

[Morris_Chair]

basically I did peak calling with MACS and now I have regions that show peaks on IGV by uploading the bam files used. I want to extract the sequences of all this peaks for multiple alignment, probably would be better to extract them from the bam files

thank you

[GenoMax]

If you have the regions marked in BED files you can extract read sequence from the region with samtools view region.

[Morris_Chair]

Do you mean the one that I obtain with MACS, summit.bed?

thanks