Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat fails with CIGAR error but read does not exist stickleback RNA Sequencing 2 06-16-2015 04:47 AM
Plot of NGS paired end distance at each genome position Retro Bioinformatics 6 04-08-2014 06:41 PM
error profile plot nanto Bioinformatics 0 09-19-2012 05:55 AM
best 16s region to amplify with NGS ? dph Metagenomics 6 07-02-2012 04:26 PM
DESeq Plot Error coralgirl Bioinformatics 2 11-29-2011 09:35 AM

Thread Tools
Old 04-20-2016, 03:22 PM   #1
Junior Member
Location: USA

Join Date: Apr 2016
Posts: 1
Default ngs.plot error: The combination of genome and region does not exist


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.


poojagangras23 is offline   Reply With Quote
Old 04-20-2016, 11:55 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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.
dpryan is offline   Reply With Quote
Old 03-13-2018, 09:56 PM   #3
Junior Member
Location: NYC

Join Date: Jul 2014
Posts: 2

were you able to figure this out. I get the same msg when selecting mm10
lmolla is offline   Reply With Quote

bioinformatic analaysis, ngs analysis platform, ngs.plot, rip-seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:05 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO