Question: Create a library of fragments from restriction enzyme AAGCTT
0
gravatar for dzisis1986
2.2 years ago by
dzisis198620
dzisis198620 wrote:

Hi

i want to create a fasta file using the mouse (mm10) genome and my first restriction enzyme AAGCTT. The new fasta file will start with AAGCTT and end with that. i already tries to create fragments with 2 existing functions of Basic4Cseq and FourCseq but without success. I want something that will list all of the AAGCTT sites in the genome in the format chr:start-stop. After that i can use this file to extract fasta sequence which will start and end with my restriction enzyme

Any idea ? any script ?

Best

Dimitris

ADD COMMENTlink written 2.2 years ago by dzisis198620
1

You can use EMBOSS restrict to do this analysis. Get the start:stop from results file. Then use samtools faidx of pyfaidx to retrieve fasta sequences from your genome file.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax85k

see Genomic Restriction Finder

ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum129k

I cant run make biostar86480 !! i installed 3 times java and again i have the same error

  /home/dimitris/jvarkit/src/main/java/com/github/lindenb/semontology/Term.java:11: error: package javax.annotation is not visible
@javax.annotation.Generated(value="xslt",date="2017-04-06T09:53:14+02:00",comments="generated from https://github.com/lindenb/semontology")
      ^
  (package javax.annotation is declared in module java.xml.ws.annotation, which is not in the module graph)
1 error
Makefile:878: recipe for target '/home/dimitris/jvarkit/dist/annotproc.jar' failed
make: *** [/home/dimitris/jvarkit/dist/annotproc.jar] Error 1

Any alternative solution ???

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by dzisis198620

you're using the wrong version of java. don't use the new java 9, or the very new java 10

http://lindenb.github.io/jvarkit/Biostar86480.html

java compiler SDK 1.8 (NOT the old java 1.7 or 1.6) and avoid OpenJdk, use the java from Oracle. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Pierre Lindenbaum129k

What i see and i cant delete is java version javac 10.0.1

ADD REPLYlink written 2.2 years ago by dzisis198620

I don't know if it's going to work with javac 10, but try to add the source and target flags in

https://github.com/lindenb/jvarkit/blob/master/Makefile#L885

 ${JAVAC} -source 1.8 -target 1.8  -d ${tmp.dir} (....)

and

https://github.com/lindenb/jvarkit/blob/master/Makefile#L106

${JAVAC}  -source 1.8 -target 1.8 \
ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Pierre Lindenbaum129k
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