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Hello Tophat user,
I run the tophat fusion on my RNA seq data. I want to load my accepted_hits.sam to the IGV browser. So trying to convert the sam file to the bam file with samtools view. But I get some errors because of the fusion reads.
[samopen] SAM header is present: 25 sequences.
[sam_read1] reference 'chr10-chr2' is recognized as '*'.
Parse error at line 37: invalid CIGAR operation
Aborted
Is there any other way to convert the file, without removing the fusion reads?
Thanks.
I run the tophat fusion on my RNA seq data. I want to load my accepted_hits.sam to the IGV browser. So trying to convert the sam file to the bam file with samtools view. But I get some errors because of the fusion reads.
[samopen] SAM header is present: 25 sequences.
[sam_read1] reference 'chr10-chr2' is recognized as '*'.
Parse error at line 37: invalid CIGAR operation
Aborted
Is there any other way to convert the file, without removing the fusion reads?
Thanks.