Alignment and splice Junctions

[akhilvelluva]

Hi,
To display bam and splice junctions in a single window I used the following code

        const options = {
        locus: locus,
        genome: 'hg38',
        tracks: [
            {
               type: 'merged',
                name: sampleid,
                height: 150,
                tracks: [
              {
               type: 'alignment',
              format: 'bam',
              url: bamUrl,
              indexURL:bamUrlindex
               },
                  
       
                    {
                        type: 'spliceJunctions',
                        format: 'bed',
                        url:bedUrl,
                        indexURL:bedIndexUrl,
                        displayMode: 'COLLAPSED',
                        // other configuration options
                         minUniquelyMappedReads: 1,
                  minTotalReads: 1,
                  maxFractionMultiMappedReads: 1,
                  minSplicedAlignmentOverhang: 0,
                  thicknessBasedOn: 'numUniqueReads', //options: numUniqueReads (default), numReads, isAnnotatedJunction
                  bounceHeightBasedOn: 'random', //options: random (default), distance, thickness
                  colorBy: 'isAnnotatedJunction', //options: numUniqueReads (default), numReads, isAnnotatedJunction, strand, motif
                  labelUniqueReadCount: true,
                  labelMultiMappedReadCount: true,
                  labelTotalReadCount: false,
                  labelMotif: false,
                  labelIsAnnotatedJunction: " [A]",
                  hideAnnotatedJunctions: false,
                  hideUnannotatedJunctions: false,
                  hideMotifs: ['GT/AT', 'non-canonical'], //options: 'GT/AG', 'CT/AC', 'GC/AG', 'CT/GC', 'AT/AC', 'GT/AT', 'non-canonical'
                    }
                ]
            }
        ]
    };

I am getting an error "error loading data", but it is working with bigwig format.

Any suggestion?

Thank you

[jrobinso]

There's not enough information there to help, what messages do you see in the console? Also, can you load the tracks individual (i.e. not as a merged file)? In particular can you load the bam file individually?

The "merged" track is not designed for use with bam files and even if you get it to load its not going to work visually. I suggest you not merge these tracks.

[akhilvelluva]

Thanks. I loaded tracks individually and it worked