IGV vs UCSC and comparison
I I have an RNA-seq data and trying to load the sorted.bam files to the IGV. when it is loaded some of the genes can not be seen meaning for instance when I check for GAPDH there are a lot of reads there and I can check different parts of that but there are some genes that no read is mapped to them and it shows nothing. I made bam files and loaded them on UCSC. then I could check those genes as well as GAPDH. do you know why I can not check some of the genes on IGV but I can do that on UCSC? how can I solve the problem on IGV? BTW, I am checking some mutations.
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Can you confirm that you are using the correct genome version (same as the one used for generation of
BAMfiles)? If the genome version is same, you can try UCSCGTFfile. Perhaps the defaultGTFfile on IGV does not have the gene annotated.