Hello! I have a few relative comparison bulk RNA-seq datasets. Generally sort and index the bam files (BW as well) for use with UCSC genome browser. This allows the investigator to look for interesting regions that correspond to genes which are differentially expressed. What would be nice would be to create a set of pileups from areas around these genes, using the sequence data, for the relative comparison and submit these to AlphaGenome and perhaps obtain the change in the model. There are lots of tutorials to make the pileups from BAM file for GATK and picardtools, but not much for importing this kind of data into AlphaGenome? It would be nice to make one model per DE gene region. The most difficult part (for me) would be proper format for the input data. Can you point me in the best direction for this? I am 100% that this would help other people. TIA
So I was just thinking that you could make it even easier if it were possible to export the region using the UCSC table browser into a format that could be easily used by AlphaGenome. Here is the UCSC table browser specs, UCSC Genome Browser Table Browser Tutorial