Can I get the intergenic regions if I have these files?

sorry if I do not know much about this

NC_000001.11    RefSeq  region  1   248956422   .   +   .   ID=NC_000001.11:1..248956422;Dbxref=taxon:9606;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA
NC_000001.11    BestRefSeq  pseudogene  11874   14409   .   +   .   ID=gene-DDX11L1;Dbxref=GeneID:100287102,HGNC:HGNC:37102;Name=DDX11L1;description=DEAD/H-box helicase 11 like 1;gbkey=Gene;gene=DDX11L1;gene_biotype=transcribed_pseudogene;pseudo=true

this is a .gff file

 SW     perc    perc    perc  query           position in query                   matching       repeat           position in repeat
score     div.    del.    ins.  sequence        begin      end             (left)   repeat         class/family   begin  end    (left)     ID

  463    1.300   0.600   1.700  NC_000001.11         10001      10468 (248945954) + (TAACCC)n      Simple_repeat       1    463    (0)      1
 3394   15.000   1.400   4.700  NC_000001.11         10469      11447 (248944975) C TAR1           Satellite/subtelo  (399)    947      1      2
  451   25.100  15.200   0.000  NC_000001.11         11505      11675 (248944747) C L1MC           LINE/L1        (2299)   5648   5452      3
  229   30.400   1.900   1.000  NC_000001.11         11678      11780 (248944642) C MER5B          DNA/hAT-Charlie   (74)    104      1      4

and this one is a .out

Can I get the intergenic regions and as in the case that I can? I mostly use awk and bedtools

genome

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updated 7.3 years ago by GenoMax

• written 7.3 years ago by kiomix106 •

Hello kiomix106!

Questions similar to yours can already be found at:

Get intronic and intergenic sequences based on gff file

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written 7.3 years ago by ATpoint

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