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Results for "
BEDtools
"
Wire posts
Jit
@jit.aber
Get the fasta sequence of the coordinates http://
bedtools
.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #
Bedtools
2612 days ago
Jit
@jit.aber
Bedtools
wiki https://code.google.com/archive/p/
bedtools
/wikis/Usage.wiki #Wiki #
Bedtools
2521 days ago
Jit
@jit.aber
get the fasta genes using gff3 and genome.fa sequence: ~/Tools/
bedtools
2/bin/
bedtools
getfasta -fi vaga.fa -bed Adineta_vaga.v2.gff3 -fo Adineta_vaga_genes.fa
2298 days ago
Rahul Nayak
@rahul
Get the sequences using coordinates in bed file. $
bedtools
getfasta -fi input_file.fa -bed regions_file.bed #Bed #Extract #Sequence #
bedtools
2241 days ago
Jit
@jit.aber
#Zero coverage regions ~/Tools/
bedtools
2/bin/
bedtools
genomecov -ibam PvsH_aln_sorted.bam -bga | awk '$4==0' > ZERO_coverage_regions.txt
2141 days ago
Abhimanyu Singh
@abhimanyu
#Intersect your bed data with coverage $
bedtools
genomecov -ibam aln.bam -bga | awk '$4==0' |
bedtools
intersect -a cds.bed -b - -f 1.0
1995 days ago
Rahul Nayak
@rahul
make a window of 60k of bed file. $
bedtools
makewindows -g genome -w 60000 > 60K.windows.bed #bed #bin #window
1939 days ago
Rahul Nayak
@rahul
Merge overlapping bed file https://
bedtools
.readthedocs.io/en/latest/content/tools/merge.html #bed #merge #overlapping
1939 days ago