Cuffcompare protocol, error of sintax in awk command
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Entering edit mode
7.3 years ago
tiago211287 ★ 1.4k

I am using Cuffcompare to identify novel and know transcripts from my cufflinks assemblies. In the paper from Nature protocols: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html there is a command in awk like this for: "printing a simple table for each assembly that lists how many transcripts in each assembly are complete matches to known transcripts".

$ for I in 'find . -name *.tmap'; do echo $i; awk 'NR  >  1 { s[$3] +  +  } END { \
                  for (j in s) { print j, s[j] }} ' $i; done;

Then, I get an error:

$ for I in 'find . -name *.tmap'; do echo $i; awk 'NR  >  1 { s[$3] +  +  } END {
for (j in s) { print j, s[j] }} ' $i; done;

find . -name *.tmap
awk: NR  >  1 { s[$3] +  +  } END {
awk:                        ^ syntax error

Unfortunately I don't know how to use awk and can't for my own know what can be causing this error. Maybe a different version of awk? Can someone help me?

$ awk --version
GNU Awk 3.1.7
Copyright (C) 1989, 1991-2009 Free Software Foundation.

Thank you for your support.

RNA-Seq cuffcompare awk • 1.5k views
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Entering edit mode
7.3 years ago
tiago211287 ★ 1.4k

Found the answer. The problem in awk was in the spaces here { s[$3] + + }, making it {s[$3]++}, solved.

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