Off topic:Can I get the intergenic regions if I have these files?
0
0
Entering edit mode
5.0 years ago
kiomix106 ▴ 10

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 • 545 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1766 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6