Hi,
I'm having some issues with removing the self ligated fragments. It seems like the grep command is working but I'm running in to issues with the sed command here is the input and the error I am getting:
$ for file in ./bedGraph/c1fos.bedGraph; do grep -v -E 'chr1.100025152.100025177|chr1.100038369.100038394' "$file" > "$(echo $file | sed 's/.bedGraph/_rm_self_und.bedGraph/g')"; done
bash: ._rm_self_und.bedGraph/c1fos_rm_self_und.bedGraph: Not a directory
Hi, I'm having some issues with removing the self ligated fragments. It seems like the grep command is working but I'm running in to issues with the sed command here is the input and the error I am getting:
$ for file in ./bedGraph/c1fos.bedGraph; do grep -v -E 'chr1.100025152.100025177|chr1.100038369.100038394' "$file" > "$(echo $file | sed 's/.bedGraph/_rm_self_und.bedGraph/g')"; done bash: ._rm_self_und.bedGraph/c1fos_rm_self_und.bedGraph: Not a directory