Question: SAM to BAM conversion
gravatar for kgauthie
3.4 years ago by
European Union
kgauthie0 wrote:

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: Exception in thread "main" java.lang.IllegalArgumentException: Invalid fastq character:  at htsjdk.samtools.SAMUtils.fastqToPhred( 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,

sam to bam • 1.2k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by kgauthie0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If the externally generated file is not to specification, there is not much that can be done except to re-run the analysis to produce a valid format. This would be possible using a Cloud Galaxy with the tool htseq installed from the Tool Shed.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k
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