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Bedtools documentation states that one can add two extra fields to a bedpe file when using bamtobed. Does anyone know how to do that? I need to add the read sequences. Thanks.
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one possible solution is to use your bed output in conjunction with
bedtools getfasta -tab
then parse the output to get the bed formatting back by perl -wpl -i.bak -e 's/:|-/\t/g;'
if you need the reads themselves and not the genome sequence where they mapped, you could write a sam parser to simply print some of the columns of the sam file. all the info you need is in the sam, just need to look at the sam docs to figure out what you want to print (i.e. which columns) and how to modify the sam to get bed-like coordinates. awk is good for such a task, just be aware of the strand
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