Hi,
I have aligned my RNA-immunoprecipitation-seq (RIP-seq) data to the zebrafish Zv9 genome. I am trying to obtain a plot showing coverage of my reads on different parts of an exon. (I expect majority of my reads to align to the last 1/3rd of exons in case of every gene).
This is my command : ngs.plot.r -G Zv9 -R exon -C ~/alignments/ripseq_IP_final/tophat2repZv9/accepted_hits.bam -O ~/ngsplot/Y14_RIPseq.exon -T Dr_Y14_RIPseq -FL 90
I have added the path of the folder where I have installed the ngs.plot compatible files of Zv9 genome to the batch script. I even created the NGSPLOT variable.
I get this error when I try to run the batch script:
Configuring variables...Error in SetupPlotCoord(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, progpath, :
The combination of genome and region does not exist. You
may need to install the genome or the region does not exist yet.
Execution halted
I do not understand why I get this error! Please help me out; I am new to NGS data analysis.
Thanks,
Pooja
I have aligned my RNA-immunoprecipitation-seq (RIP-seq) data to the zebrafish Zv9 genome. I am trying to obtain a plot showing coverage of my reads on different parts of an exon. (I expect majority of my reads to align to the last 1/3rd of exons in case of every gene).
This is my command : ngs.plot.r -G Zv9 -R exon -C ~/alignments/ripseq_IP_final/tophat2repZv9/accepted_hits.bam -O ~/ngsplot/Y14_RIPseq.exon -T Dr_Y14_RIPseq -FL 90
I have added the path of the folder where I have installed the ngs.plot compatible files of Zv9 genome to the batch script. I even created the NGSPLOT variable.
I get this error when I try to run the batch script:
Configuring variables...Error in SetupPlotCoord(args.tbl, ctg.tbl, default.tbl, dbfile.tbl, progpath, :
The combination of genome and region does not exist. You
may need to install the genome or the region does not exist yet.
Execution halted
I do not understand why I get this error! Please help me out; I am new to NGS data analysis.
Thanks,
Pooja
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