JAFFA
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Oshlack
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
Hi all, I've analyzed the simulated demo data using JAFFAL and the program successfully detected the fusion transcript. Now I want to use JAFFAL to analyze Nanopore data to identify...
Hello, I am currently testing JAFFAL and other long-read fusion finding tools on a simulated dataset ~generated using badread to simulate reads and FUSIM to simulate fusions (including tri-fusions). The...
Hello @nadiadavidson, We have an FFPE sample that was positive for BCOR-CCNB3 fusion. We have performed RNA sequencing for the same using nanopore technologies. I was not able to get...
Hi, there is an error shows when run process_transcriptome_align_table. Any solutions? Thank you. Done reading in transcript IDs Reading the input alignment file, AP169/AP169.paf 0 terminate called after throwing an...
Dear JAFFA Developer, I encountered a java.lang.ExceptionInInitializerError with the following stack trace: `at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109) at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131) Caused by: groovy.lang.MissingMethodException: No signature...
Hi all, I am using JAFFA-2.4 to discover the BCL2 fusions in FFPE target RNA sequencing data. While this sample had been verified positive using FISH, with partener gene IGHJ,...
Hi there, nice job! i already install the tools and all steps perfectly installed , but running it on my own data or on the provided data(simulated one) im getting...
Dear JAFFA developper, I managed to make a docker image for JAFFA version 2.3 that is nearly working for me. One of the last step (that comes after the final...
Hi, I am using JAFFAL for the first time and trying to run it with multiple threading. I have used the following command but looks like multiple threading is not...
Hi there, I'm trying to run jaffal from the Biocontainers Docker container, which is built automatically from the Jaffa conda. I see that there are wrapper scripts for running jaffa-assembly,...
