Question: IGV vs UCSC and comparison
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gravatar for Sara
2.7 years ago by
Sara90
Sara90 wrote:

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.

rna-seq • 1.3k views
ADD COMMENTlink written 2.7 years ago by Sara90

Can you confirm that you are using the correct genome version (same as the one used for generation of BAM files)? If the genome version is same, you can try UCSC GTF file. Perhaps the default GTF file on IGV does not have the gene annotated.

ADD REPLYlink written 2.7 years ago by Satyajeet Khare1.5k
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