Hi~How can I get the cit file?

erhard-lab / gedi

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Hi~How can I get the cit file? #9

Closed LongYuan0529 closed 5 months ago

LongYuan0529 commented 6 months ago

I already have bam file, how can I get the cit file? I have already tried to use gedi -e Bam2CIT, but the error is "SEVERE Could not load startup FxStartup.class in./gedi.jar Exception in thread "main"java.lang.UnsupportedOperationException:Cannot query SAM text files at htsjdk.samtools.SAMTextReader.query(SAMTextReader.java:183)" Thanks a lot!

florianerhard commented 5 months ago

Dear LongYuan0529, as the error message says, it cannot work with sam text files. Please convert to bam first (and you also need to sort and index)! Best, Florian