Can't create indexes using create_indexes_from_ucsc.pl RUM aligner perl script

Question

[bioinfo89]

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!!

[Kevin Blighe]

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.

[bioinfo89]

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.

[Kevin Blighe]

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

[bioinfo89]

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??