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Question: SAM to BAM conversion
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gravatar for kgauthie
3.4 years ago by
kgauthie • 0
European Union
kgauthie • 0 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: -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,
sam to bam • 1.2k views
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modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by kgauthie • 0
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gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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. https://wiki.galaxyproject.org/BigPicture/Choices

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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