I have a tool that performs alignment against a reference sequence and then creates an IGV session file based on that alignment and other features of the reference sequence.
<Global> genome="dataset_18581.dat" locus="dataset_18581.dat" version="3" <Resources> <Resource name="726173-1-1 align" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//726173-1-1-1510602244-bowtie2.bam.sort.rmdup.bam.sort.bam"/> <Resource name="726173-1-1 variants" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//726173-1-1-1510602244-bowtie2.bam.sort.rmdup.bam.sort.bam.vcf"/> <Resource name="726173-1-1 zero coverage gaps" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//726173-1-1-1510602244-zero_coverage_gaps.bedgraph"/> <Resource name="726173-1-1 below threshold coverage gaps" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//726173-1-1-1510602244-below_threshold_coverage_gaps.bedgraph"/> <Resource name="726173-1-1 zero anchored coverage gaps" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//anchored-726173-1-1-1510602244-zero_coverage_gaps.bedgraph"/> <Resource name="726173-1-1 below threshold anchored coverage gaps" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//anchored-726173-1-1-1510602244-below_threshold_coverage_gaps.bedgraph"/> <Resource name="726173-1-1 soft clipping" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//COT102Frag1F4R1.txt-1510602244-soft_clipping.bedgraph"/> <Resource name="726173-1-1 non-ref frequency" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//COT102Frag1F4R1.txt-1510602244-non-ref_freq.bedgraph"/> <Resource name="726173-1-1 strand bias" path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//COT102Frag1F4R1.txt-1510602244-strand_bias.bedgraph"/> <Resource name="726173-1-1 homopolymers " path="http://demeter//project/LEE2705/TEST/TK0000000/171013_M01610_0074_000000000-D30NY/726173-1-1/1510602244//COT102Frag1F4R1.txt-1510602244-homopolymers.bedgraph"/> </Resources> </Global>
I have used this several times and it has worked fine. However, I have a dataset now where several of these tracks are not rendered though they are uploaded (because they are present in the track window) and they are read by IGV (since the displayed data range is correct for each track that contains data (not all do)). For this dataset the reference is small (1426bp) and the reads are 250bp PE. The alignment (bam) and coverage tracks seem to render properly but tracks showing strand bias and homopolymers (which contain data) are empty. I can zoom in as far as possible at locations where features should appear but there is nothing. Likewise no choice of "windowing function" makes them appear either.