Excluding or including by awk












2












$begingroup$


I have a gtf file as attached enter link description here



By this command one could extract coding parts of genome 



awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


How I could exclude coding parts from this file keeping non coding regions






linux wgs bash







share|improve this question









$endgroup$

















    2












    $begingroup$


    I have a gtf file as attached enter link description here



    By this command one could extract coding parts of genome 



    awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


    How I could exclude coding parts from this file keeping non coding regions






    linux wgs bash







    share|improve this question









    $endgroup$















      2












      2








      2


      1



      $begingroup$


      I have a gtf file as attached enter link description here



      By this command one could extract coding parts of genome 



      awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


      How I could exclude coding parts from this file keeping non coding regions






      linux wgs bash







      share|improve this question









      $endgroup$




      I have a gtf file as attached enter link description here



      By this command one could extract coding parts of genome 



      awk '{if($3=="transcript" && $20==""protein_coding";"){print $0}}' gencode.gtf


      How I could exclude coding parts from this file keeping non coding regions






      linux wgs bash




      linux wgs bash






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked 2 hours ago









      Feresh TehFeresh Teh

      38111




      38111






















          1 Answer
          1






          active

          oldest

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          3












          $begingroup$

          Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



          UTR has its own feature in the gtf file. So you can do this:



          $ awk -v FS="t" '$3=="UTR"' gencode.gtf


          If the gtf file is compressed use this instead:



          $ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


          BTW: Why are you using such an old release of gencode? The current version is v29.






          share|improve this answer











          $endgroup$













          • $begingroup$
            Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
            $endgroup$
            – Feresh Teh
            1 hour ago










          • $begingroup$
            Sorry I tried hat but my output is empty
            $endgroup$
            – Feresh Teh
            1 hour ago






          • 1




            $begingroup$
            As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
            $endgroup$
            – finswimmer
            1 hour ago












          • $begingroup$
            Thank you but both of your commands return nothing :(
            $endgroup$
            – Feresh Teh
            1 hour ago











          Your Answer





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          1 Answer
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          active

          oldest

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          3












          $begingroup$

          Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



          UTR has its own feature in the gtf file. So you can do this:



          $ awk -v FS="t" '$3=="UTR"' gencode.gtf


          If the gtf file is compressed use this instead:



          $ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


          BTW: Why are you using such an old release of gencode? The current version is v29.






          share|improve this answer











          $endgroup$













          • $begingroup$
            Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
            $endgroup$
            – Feresh Teh
            1 hour ago










          • $begingroup$
            Sorry I tried hat but my output is empty
            $endgroup$
            – Feresh Teh
            1 hour ago






          • 1




            $begingroup$
            As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
            $endgroup$
            – finswimmer
            1 hour ago












          • $begingroup$
            Thank you but both of your commands return nothing :(
            $endgroup$
            – Feresh Teh
            1 hour ago
















          3












          $begingroup$

          Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



          UTR has its own feature in the gtf file. So you can do this:



          $ awk -v FS="t" '$3=="UTR"' gencode.gtf


          If the gtf file is compressed use this instead:



          $ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


          BTW: Why are you using such an old release of gencode? The current version is v29.






          share|improve this answer











          $endgroup$













          • $begingroup$
            Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
            $endgroup$
            – Feresh Teh
            1 hour ago










          • $begingroup$
            Sorry I tried hat but my output is empty
            $endgroup$
            – Feresh Teh
            1 hour ago






          • 1




            $begingroup$
            As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
            $endgroup$
            – finswimmer
            1 hour ago












          • $begingroup$
            Thank you but both of your commands return nothing :(
            $endgroup$
            – Feresh Teh
            1 hour ago














          3












          3








          3





          $begingroup$

          Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



          UTR has its own feature in the gtf file. So you can do this:



          $ awk -v FS="t" '$3=="UTR"' gencode.gtf


          If the gtf file is compressed use this instead:



          $ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


          BTW: Why are you using such an old release of gencode? The current version is v29.






          share|improve this answer











          $endgroup$



          Getting the non coding regions of a protein coding transcript, sounds like you are looking for UTR.



          UTR has its own feature in the gtf file. So you can do this:



          $ awk -v FS="t" '$3=="UTR"' gencode.gtf


          If the gtf file is compressed use this instead:



          $ zcat gencode.gtf.gz | awk -v FS="t" '$3=="UTR"'


          BTW: Why are you using such an old release of gencode? The current version is v29.







          share|improve this answer














          share|improve this answer



          share|improve this answer








          edited 1 hour ago

























          answered 1 hour ago









          finswimmerfinswimmer

          962210




          962210












          • $begingroup$
            Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
            $endgroup$
            – Feresh Teh
            1 hour ago










          • $begingroup$
            Sorry I tried hat but my output is empty
            $endgroup$
            – Feresh Teh
            1 hour ago






          • 1




            $begingroup$
            As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
            $endgroup$
            – finswimmer
            1 hour ago












          • $begingroup$
            Thank you but both of your commands return nothing :(
            $endgroup$
            – Feresh Teh
            1 hour ago


















          • $begingroup$
            Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
            $endgroup$
            – Feresh Teh
            1 hour ago










          • $begingroup$
            Sorry I tried hat but my output is empty
            $endgroup$
            – Feresh Teh
            1 hour ago






          • 1




            $begingroup$
            As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
            $endgroup$
            – finswimmer
            1 hour ago












          • $begingroup$
            Thank you but both of your commands return nothing :(
            $endgroup$
            – Feresh Teh
            1 hour ago
















          $begingroup$
          Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
          $endgroup$
          – Feresh Teh
          1 hour ago




          $begingroup$
          Sorry, literally I need non coding regions of human genome, but for asking my question here I referred to coding parts too
          $endgroup$
          – Feresh Teh
          1 hour ago












          $begingroup$
          Sorry I tried hat but my output is empty
          $endgroup$
          – Feresh Teh
          1 hour ago




          $begingroup$
          Sorry I tried hat but my output is empty
          $endgroup$
          – Feresh Teh
          1 hour ago




          1




          1




          $begingroup$
          As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
          $endgroup$
          – finswimmer
          1 hour ago






          $begingroup$
          As @Wouter tells you, the non coding region of a genome is the complement of the coding regions. Coding regions have its own feature in the gtf file. You can get them with $ awk -v FS="t" '$3=="CDS"' gencode.gtf. Reading the manual for bedtools complement is your task.
          $endgroup$
          – finswimmer
          1 hour ago














          $begingroup$
          Thank you but both of your commands return nothing :(
          $endgroup$
          – Feresh Teh
          1 hour ago




          $begingroup$
          Thank you but both of your commands return nothing :(
          $endgroup$
          – Feresh Teh
          1 hour ago


















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