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awk format question

I have a gene list txt file and need to format it to tab-delimit file. The list has six columns: chr, startPos,endPos, width, strand, name The code is awk '{printf("%s\t%s\t%s\t%s\t%s\t%s\t\n",$1,$2,$3,$4,$5,$6)};' input.txt > output.txt Then I ran some codes, the result said that 'Perhaps you have non-integer starts or ends at line 1?' I used ' cat -e file |more' to check the lines, each line has addition (tab) $ at the end.

ex. chr12<tab>1234<tab>456<tab>789<tab>+<tab>TP53<tab>$ Please let me know where is wrong. Thanks in advance.

awk bed format
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updated by GenoMax GenoMax • written by newbiebio newbiebio

1 answer

It isn't related to the error, probably, but you print an extra and unnecessary tab at the end of each line:

awk '{printf("%s\t%s\t%s\t%s\t%s\t%s\t\n",$1,$2,$3,$4,$5,$6)};' input.txt > output.txt
                                    ^
                                    |

I'm not sure what the error message means, but in your example, there are a few potential problems:

  1. The end coordinate is smaller than the start coordinate.
  2. The name ("ID") generally goes into the fourth column.
  3. The score or some numerical value generally goes into the fifth column.
  4. The strand generally goes into the sixth column.

Most of these issues can be fixed with a few tweaks, like reordering the field variables $2 through $6. If you can post the actual output of running the above on your true input.txt file, that may help figure out what the real issue is.

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written by Alex Reynolds Alex Reynolds

I removed the '\t' you printed out, the '$' is still at the end of each line. The result like 'chr12<tab>1234<tab>456<tab>789<tab>+<tab>TP53$' now. But I will check each column as you suggested. And see if it works. Thank you very much for your suggestion.

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written by newbiebio newbiebio

The $ is just a symbol to show the newline character, which is correct. I would recommend checking the order of $2 through $6.

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written by Alex Reynolds Alex Reynolds

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