[miso-users] miso file format

[Yarden Katz]

The problem might be in BAM file. Your BAM has headers like:

AT4G38040.1

In the chromosome position.  If your annotation says that, for example, AT4G38040.1 is on "chr1", then it will try to fetch it from chr1 in the BAM.  Unless the chr headers appear in your BAM somewhere else in the file, MISO won't be able to find it.  If your BAM has some alignments that align to extra chromosome headers like AT4G38040.1 in addition to alignments to align to the chr* chromosomes in your annotation, then this is fine, and the output you got just means that for the gene "AT3G15020" has no alignments. 

In short, it still looks to me like your BAM has different headers from your GFF, unless the GFF headers appear later in the BAM file and not in the segment you've shown. 

  --Yarden


On Dec 20, 2012, at 10:05 PM, mykhwab wrote:

> AT4G38040.1