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Old 06-30-2016, 02:10 AM   #4
pengchy
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Location: China

Join Date: Feb 2009
Posts: 116
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Quote:
Originally Posted by clarissaboschi View Post
Thanks Colindaven, yes I was thinking that the issue is on my QTL file that I got from a database.
I already found different issues in this file, like start position bigger than end position and also lines with no positions, but I will do more checks!
Hi, the problem is caused by the redundancy of the QTL file. There are many line with the same start and end position, if you using the abbreviation as ID, there will be all the same, just like the following lines:

Code:
1       7232667 7273886 DRIPL   +
1       7232667 7273886 DRIPL   +
you can use "sort -u" to remove the redundancy.

Another reason is the NULL position, like the following line:
Code:
Chr.10  Animal QTLdb    Meat_and_Carcass_Association                    .       .       .       QTL_ID=65998;Name=Juiciness score;Abbrev=JUICE;PUBMED_ID=22297614;trait_ID=65;trait=Juiciness score;breed=yorkshire;FlankMarkers;PTO_name=meat juiciness;Map_Type=Linkage;Model=Mendelian;Test_Base=-;peak_cM=73.1;Significance=Significant;P-value=0.0433;gene_ID=100517235;gene_IDsrc=NCBIgene
Just remove these lines.

Last edited by pengchy; 07-04-2016 at 04:31 PM.
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