extract multiples regions from IGV
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 :)
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Morris_Chair
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From IGV or BAM? Do you want sequence from BAM or screenshots from IGV for regions you are interested in?
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
If you have the regions marked in BED files you can extract read sequence from the region with
samtools viewregion.Do you mean the one that I obtain with MACS, summit.bed?
thanks