I have seen that I am not the first one to have the problem: the SAM to BAM conversion (either directly using "Edit attribute" or the Main Menu) does not work and I received an error message. (Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Exception in thread "main" java.lang.IllegalArgumentException: Invalid fastq character: at htsjdk.samtools.SAMUtils.fastqToPhred(SAMUtils.java:419) at hts"
I also checked your advise to a previous post and nothing works: The ReorderSam function leads to the same error message. The SAM file was generated within Galaxy from a htseq file downloaded from EBI using BWA. It seems that the quality column is not properly filled by BWA. What can I do?
Thank you for your help,