Question: extraxt interval from maf
gravatar for Nobody
4.0 years ago by
Nobody0 wrote:

I have a maf file like this :

##maf version=1
# 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? 



alignment • 952 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Nobody0
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 COMMENTlink written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k

Perfect it worked

ADD REPLYlink written 4.0 years ago by Nobody0

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 REPLYlink written 4.0 years ago by Nobody0
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