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nextgenusfs / augustus

AUGUSTUS v3.2.1 for installation on Mac OS X
GNU General Public License v3.0
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Bam2hints produces an empty hint file #3

Closed Jung19911124 closed 6 years ago

Jung19911124 commented 6 years ago

Hi.

I am trying to make intron hints from multiple RNA-seq data set with augustus-v3.3.1, following this wiki (http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq.Tophat).

At step 9, I merged all bowtie.global.h.bam and accepted_hits.noN.bam into a single bam file. After that, at step 11, bam2hints program created an empty hints.gff file, but there was no error message.

What is wrong with my procedure?

nextgenusfs commented 6 years ago

I don’t know. But the BAM file does need to be sorted, so if you didn’t do that then I’d try that. This is not an Augustus developer repository, just one that allows for compilation on Mac.