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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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meth to bed #187

Closed hchetia closed 3 years ago

hchetia commented 3 years ago

Hi, I am trying to convert the meth file to bed for ultimately converting it to bigwigs. The command provided in the manual leads to an error-

awk: cmd. line:1: ’{print awk: cmd. line:1: ^ invalid char '?' in expression

The command used is awk -v OFS="\t" ’{print $1, $2, $2+1, $4":"$6, $5, $3}’ CpG_sorted_start.meth CpG_sorted_start.bw

Best, Hasna

andrewdavidsmith commented 3 years ago

Did you copy and paste into the terminal, or did you type it out?

hchetia commented 3 years ago

Hi @andrewdavidsmith I was copy pasting earlier, when I kept getting the error. Tried typing the whole command and it worked. Why so?