joachimwolff / chicago Goto Github PK
View Code? Open in Web Editor NEWFork of the CHiCAGO package from Babraham Institute, Cambridge hosted on bitbucket
Fork of the CHiCAGO package from Babraham Institute, Cambridge hosted on bitbucket
Hi,
I want to make oligo files of mm10.
Which script can I make??
Hi, found a bug in bam2chicago.sh, I was getting this error from bedtools:
Error: Type checker found wrong number of fields while tokenizing data line.
Perhaps you have extra TAB at the end of your line? Check with "cat -t"
Traced it back to this bit in your code
echo "Flipping all reads that overlap with the bait on to the right-hand side..."
awk 'BEGIN{ OFS="\t" }
{
minRight=$13<$3?$13:$3;
maxLeft=$12>$2?$12:$2;
if($1==$11 && (minRight-maxLeft)/($3-$2)>=0.6){
print $4,$5,$6,$1,$2,$3,$7,$8,$10,$9,$11,$12,$13,$14,$15
}
else {
print $0
}
}' ${samplename}/${bamname}_mappedToBaits.bedpe > ${samplename}/${bamname}_mappedToBaits_baitOnRight.bedpe
For some reason, you are trying to output $15
but ${samplename}/${bamname}_mappedToBaits.bedpe
only has 14 fields. Remvoing $15
from the line fixed the issue.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.