Problem with generating UCSCs refGene format

Question

[gtho123]

Hi have performed a differential expression experiment using RNA-Seq and would like to have a go with chromosome clustering. I found this program CROC which seems like it could help but it requires a list of genes (which I have) and a reference genome in UCSCs refGene format.

Since I work in on a plant with not reference refGene file to use I have tried to generate my own following advice on SeqAnswers. Essentially I used UCSCs gtfToGenePred to create a refGene file from a GTF file.

However while I can load it into CROC, when I run the clustering program it fails to identify the genes in the reference. I think there must be something wrong with my reference file as I can see the relevant gene IDS in there. How can I adjust it so that gene IDs will be picked out.

Here are the first few entries of my generated refGene file:

XLOC_000001    TCONS_00000001    chr1    +    6523    7366    7366    7366    2    6523,7097,    6620,7366,
XLOC_000002    TCONS_00000002    chr1    +    14513    15729    15729    15729    2    14513,15502,    14556,15729,
XLOC_000003    TCONS_00000003    chr1    +    16282    18382    18382    18382    3    16282,17060,18241,    16326,17304,18382,
XLOC_000004    TCONS_00000004    chr1    +    31972    32344    32344    32344    1    31972,    32344,

and I insert in Gene IDs which look like this:

XLOC_000007
XLOC_000287
XLOC_000320
XLOC_000381
XLOC_000394
XLOC_000645
XLOC_000754

I am not familiar with this file format so thought that switching the first two columns around might help. It did not.

Any help is greatly appreciated.

[brentp]

do your other results have the 'chr' prefix? e.g. are they '1' instead of 'chr1?

[gtho123]

They all have the 'chr' prefix.

These are all the values that are in that column

chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
scaffold0001
scaffold0002
scaffold0003
scaffold0004
..... 
scaffold2177