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Question: extraxt interval from maf
0
gravatar for Nobody
4.0 years ago by
Nobody • 0
Spain
Nobody • 0 wrote:

I have a maf file like this :

##maf version=1
# emf2maf.pl v1.0.1 from file /lustre/scratch109/ensembl/sf5/Compara77/39mammals_dumps/emf/Compara.17_eutherian_mammals_EPO.chr22_4.emf
# Here is the header from the orginal file:
# original dump date: Thu Aug  7 13:03:38 2014
# ensembl release: 76
# emf comment: Alignments: 17 eutherian mammals EPO
# emf comment: Region: Homo sapiens chromosome:GRCh38:22:1:50818468:1
# emf comment: File 4
s homo_sapiens.22                  40636690   42750 +   50818468 CTCCTCTCAGCCACGGA
s ancestral_sequences.Ancestor_755_853509          0   42825 +      42825 CTCCTCTCA
s pan_troglodytes.22               39344200   44198 +   49737984 CTCCTCTCAGCCACGGA-

 

And a bed file like this:

chr22 50875495   50875597  
chr22 36704854   36704959  
chr22 43276623     43276820  
chr22 43276623 43277622

 
     

 

 

 
       

When I run Extract MAF blocks given a set of genomic intervals, I do not get anything, should I change the name of the chromosome or something like that? 

 

Thanks
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modified 4.0 years ago • written 4.0 years ago by Nobody • 0
1
gravatar for Daniel Blankenberg
4.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

There are two possible issues going on:

  • The chromosome names need to match
  • You need to make sure that the dbkey of your BED file matches the name of the organism in the MAF file
     
ADD COMMENT • link written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k

Perfect it worked

ADD REPLY • link written 4.0 years ago by Nobody • 0

Have you also heard about mafsInregion, I do not know why it does not detect anything neither because I also change the name of the chromsome but db can not be changed for a bed file for mafsInregion as I do not know how to specify that :-)

ADD REPLY • link written 4.0 years ago by Nobody • 0
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