SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
To locate some introgressed QTL regions of an assembly? Dingen Bioinformatics 0 10-14-2014 02:23 PM
RAD-tag QTL annotation pfranchini Bioinformatics 0 02-04-2013 02:51 AM
Overlap number discrepancy between VCFTools and BEDTools zxyeo Bioinformatics 2 12-27-2011 04:36 PM
Qtl semna General 0 10-07-2011 05:28 AM
QTL location? semna Genomic Resequencing 0 10-07-2011 03:48 AM

Reply
 
Thread Tools
Old 06-01-2016, 05:10 AM   #1
clarissaboschi
Member
 
Location: US

Join Date: Apr 2010
Posts: 63
Default QTL overlap (bedtools)

Dear all, I am trying to compare some QTL regions with specific genome regions that I have, for it I am using bedtools.
I used before bedtools with a list of genes and it worked well, but this time I am getting the error message: "***** ERROR: too many digits/characters for integer conversion in string . Exiting...".

My input files are:
QTL file (with about 5,000 regions):
Chr1 241009 241109 GROW
Chr1 241009 241109 PLASCO
Chr1 2095900 3104645 BW
Chr1 2329958 2400142 AF
Chr1 2329958 2400142 BW


and my genomic regions input (with about 700 regions):
Chr1 18340001 18360000
Chr1 18350001 18370000
Chr1 18570001 18590000
Chr1 18960001 18980000
Chr1 18970001 18990000
Chr1 18980001 19000000

I tried different command lines, and I got the same error every time (and some times I had a output until the chromosome 8, and sometimes no result):
Code:
intersectBed -c -a QTLfile.bed  -b regionFile.bed > outfile
I am not sure what is the problem, I checked my files and it seems that they are ok....I tried also to increase the memory and split the chromosomes, and I also had the same error..

thanks

Last edited by clarissaboschi; 06-01-2016 at 12:27 PM.
clarissaboschi is offline   Reply With Quote
Old 06-02-2016, 09:02 AM   #2
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 415
Default

Sounds like an error with your input files. MAybe the separators are wrong on one line.

Try reading both files into R / Calc etc and doing some summary statistics. You'll probably find that there is a space not a tab on one line.
colindaven is offline   Reply With Quote
Old 06-02-2016, 09:54 AM   #3
clarissaboschi
Member
 
Location: US

Join Date: Apr 2010
Posts: 63
Default

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!
clarissaboschi is offline   Reply With Quote
Old 06-30-2016, 02:10 AM   #4
pengchy
Senior Member
 
Location: China

Join Date: Feb 2009
Posts: 116
Default

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.
pengchy is offline   Reply With Quote
Reply

Tags
bedtools, intersec, overlap, qtl

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO