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Old 04-20-2016, 03:22 PM   #1
poojagangras23
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Location: USA

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Default ngs.plot error: The combination of genome and region does not exist

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
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Old 04-20-2016, 11:55 PM   #2
dpryan
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Location: Freiburg, Germany

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Presumably you have different chromosome names than ngs.plot is expecting. One possibility would be to reheader the BAM file, after converting between Ensembl and UCSC chromosome names. That might solve the issue. You can find the name conversion here.
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Old 03-13-2018, 09:56 PM   #3
lmolla
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were you able to figure this out. I get the same msg when selecting mm10
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bioinformatic analaysis, ngs analysis platform, ngs.plot, rip-seq

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