Hi,
I am analyzing Danio Rerio RNA Seq data and I want to use RUM aligner for the same. I tried to create indexes for danRer10 reference genome using the perl script create_indexes_from_ucsc.pl provided by the tool (RUM) itself. But when I run the script I get the following error:
ERROR: exon for chr19:24313443-24314278 not found. chr19 - 24313442 24333896 6 24313442,24315425,24327938,24330141,24332780,24333617, 24314278,24315560,24328083,24330292,24332872,24333896, NM_199546(danRer10_RefSeqgene) i=0 at /home/kchandratre/tools/rum-master/bin/create_indexes_from_ucsc.pl line 97.
I have downloaded the RefSeq gene file from UCSC table browser.
Any help for the same would be appreciated.
Thanks!!
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Hello, what is the exact command that you are running?
Have you tried the other options here: http://www.cbil.upenn.edu/RUM/how2setup_genome-indexes_forPipeline.txt
The RUM developers provide pre-built indices for danRer7, if that would be sufficient.
Hi Kevin,
Yes I tried the other option mentioned here: http://www.cbil.upenn.edu/RUM/how2setup_genome-indexes_forPipeline.txt. After following the steps I get the above mentioned error.
I want to create indexes for danRer10.
I ran the following command to create the indexes: perl rum-master/bin/create_indexes_from_ucsc.pl danRer10_genome.txt danRer10_UCSC
I am not sure why the script is throwing this error since the input file is downloaded in the same manner mentioned in the tutorial script.
Okay, then the problem is likely that that one file is 1-based co-ordinates, whilst the other is 0-based.
chr19:24313443-24314278
chr19 - 24313442
Actually, the input file is chr19 - 24313442 but when I run the script, it looks for the exons from chr19:24313443. I am not sure how do I change this....Can you suggest anything for the same??