Extract chimeric reads

Question

[Ram]

Dear all,

I am trying to align reads to human and virus genome in one FASTA file. So is it possible to know how i can retrive the chimeric reads i.e reads align both human and virus genome ?

Thanks a lot for your help.

Answer 1

[Pierre Lindenbaum]

see Extracting chimeric reads from mapping

[Ram]

Thanks a lot for your reply.

So in case of samjdk, if i have to use full command mentioned in the post to obtain chimeric reads ?

[Ram]

Dear Pierre,

Could please suggst which java version to use. As I am using jdk1.8.0_181.jdk and it is showing error in installing samjdk.

Thanks !

[Pierre Lindenbaum]

and it is showing error in installing samjdk

so ? what is the error ?

[Ram]

Thanks for your reply.

echo '### Printing javac version : it should be Oracle 1.8 (you should avoid OpenJDK). if Not, check your ${PATH}.'
Printing javac version : it should be Oracle 1.8 (you should avoid OpenJDK). if Not, check your ${PATH}.
javac -version 2> samjdk.jdkversion && cat samjdk.jdkversion && grep -E '1\.8\.[0-9_]+' samjdk.jdkversion && rm samjdk.jdkversion

make: *** [samjdk] Error 20

[Pierre Lindenbaum]

what is the output of the simple command

javac -version

[Ram]

Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/bin/java/bin/javac" (-1)

[Pierre Lindenbaum]

your environment is not properly installed. It's not related to jvarkit.

[Ram]

Hi Pierre,

As I have solved the problem with environment. Is it possible to know if samjdk will work for single end reads ?

[Pierre Lindenbaum]

yes if the reads contain the X:SA tag ( a list of supplementary alignements )

bwa does this.

[Ram]

Thanks for replying. Yes I am using bwa itself and I have the reads with SA tag. Does SA reads are considered to be chimeric reads ?

Thanks a lot for your help.

[Pierre Lindenbaum]

yes. One part of the read maps one organism, another maps the virus.