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