Aditi Kulkarni

Hi, We are trying to use RSeQC with our RNA Seq samples. I have tried using several BED files (the hg19 one provided, the RefSeq and UCSC BED files downloaded from the folder on source forge) but none of them seem to be working. When I use the 'junction_annotation.py' module, my output shows that 100% of the transcripts assembled are novel which is not true. I am not sure what is going on and why this is the case ? Any help/thoughts on this would be highly appreciated. Thank you. Aditi Kulkarni

Hi, We are trying to use RSeQC with our RNA Seq samples. I have tried using several BED files (the hg19 one provided, the RefSeq and UCSC BED files downloaded from the folder on source forge) but none of them seem to be working. When I use the 'junction_annotation.py' module, my output shows that 100% of the transcripts assembled are novel which is not true. I am not sure what is going on and why this is the case ? Any help/thoughts on this would be highly appreciated. Thank you. Aditi Kulkarni Electronic...

Hi, We are trying to use RSeQC with our RNA Seq samples. I have tried using several BED files (the hg19 one provided, the RefSeq and UCSC BED files downloaded from the folder on source forge) but none of them seem to be working. When I use the 'junction_annotation.py' module, my output shows that 100% of the transcripts assembled are novel which is not true. I am not sure what is going on and why this is the case ? Any help/thoughts on this would be highly appreciated. Thank you. Aditi Kulkarni Bioinformatics...

Hi Cristina, This doesn't seem to work for me. I am getting the same error again. I am not sure of how to proceed with this now.

Hi Cristina, This doesn't seem to work for me. I am getting the same error again. I am not sure of how to proceed with this now.

Hi Jin Xinhao, Were you able to fix this issue ? I am running into the same issue "genomdat must be numeric" so I am wondering how you proceeded with this. Thanks.

Hi Dan, Were you able to find a fix for this issue ? Best, Aditi

Hi Dan, The command I am using is this java -jar /scratch/chadbren_flux/aditisk/New_Exomes/trimmed_reads/recal_bams/VarScan.v2.4.1.jar...