Maps (Barley Vs Rice Genome)

[Sharon Wei]

Thanks for being interested in gramene mapping. Please find the updated 
mapping in the attachment.

The format of this file is as follows:
Hit_id   
Feature_Name       
Chr_segment(may be ignored)
Chr_strand
Feature_start
Feature_end 
Chromosome
Chr_start
Chr_end  
score(may be ignored)  
perc_id(may be ignored) 
CIGAR(may be ignore)

1       Barley1_00002   chr_4_6 1       1       72      4       
33022121        33022192        261     86      71M
1       Barley1_00002   chr_4_6 1       155     294     4       
33022293        33022432        261     86      139M
1       Barley1_00002   chr_4_6 1       323     459     4       
33022565        33022701        261     86      136M

Please be aware of the following coordinates changes:

# The alignment feature query coordinates changed in this release

    * The alignment block coordinates no longer follow the BLAT output
      format, where the query coordinates are from the point of view of
      the reverse strand when the match is on the reverse strand. The
      query coordinates are always on the forward strand.
    * All the coordinates are 1-based for both feature and chromosome.


You are right, the rice genome is the 3rd version from Tigr.
The files in ftp://ftp.gramene.org/pub/gramene/array_mapping/ are old 
alignment between chips and rice genome,
they are not the updated mapping.

Please feel free to ask if any more questions come up.


Sharon
Gramene Project


Hong Lu wrote:

>Hello,
>
>I am a graduate student at Iowa State University. I am interested in alignment
>between plant genechips and rice genome. Last year I got alignment between
>barley and rice genome from Gramene. But now, when I check it, I find it has
>been updated. Would you like to send my the latest alignment file? Thanks. The
>format I got last time is as below,
>
>Hit_id	Feature_name	Chr_segment (may be ignored)	Strand	Feature_start
>Feature_stop	Chromosome	Chr_Start	Chr_end
>1	Barley1_00002	9632:30000001..34960948	1	0	72	4	32959322	32959394
>1	Barley1_00002	9632:30000001..34960948	1	154	294	4	32959494	32959634
>1	Barley1_00002	9632:30000001..34960948	1	322	459	4	32959766	32959903
>2	Barley1_00006	9629:25000001..30000000	1	736	788	1	29809574	29809632
>
>What's the version of rice genome that aligns those chips? The 3rd version from
>Tigr?
>ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_3.0/
>
>In the directory ftp://ftp.gramene.org/pub/gramene/array_mapping/, I find 4
>alignment files. Are those the alignment between chips and rice genome(ver 3)? 
>
>Thanks you for your help and I am looking forward to hearing from you.
>
>Hong
>
>
>  
>

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