Results for "gff"
Bio-Scripts
Download the gff files from NCBI using bash script/command
...Create a Directory mkdir genome_gff cd genome_gff # Look for genome assembly.../all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_fungi.../all/.+/)(GCA_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_bacteria.../all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_protozoa...2519 days ago
Plot custom gene density with R
library(karyoploteR) pp2245 days ago
Perl script to convert GFF 2 FASTA !
...$ARGV[0]; my $db = Bio::DB::Fasta->new($file_fasta); print ("Genome fasta parsed\n"); ### Second, parse the GFF3 my %CDS; my %CDNA; my $mRNA_name; my $frame; open GFF, "...2135 days ago
- ...home/urbe/Tools/Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04.break echo "[REAPR p...home/urbe/Tools/Reapr_1.0.18/reapr break 00.assembly.fa 03.score.errors.gff.gz 04.break echo "[REAPR p...
2095 days ago
- library(vcfR) # Input the files. vcf
2056 days ago
- ...-1.9/test/tabix/ htslib-1.9/test/tabix/bed_file.Y.100200.out htslib-1.9/test/tabix/bed_file.bed htslib-1.9/test/tabix/gff_file.X.2934832.2935190.out htslib-1.9/test/tabix/gff_file.gff htslib-1.9/test/tab...
2015 days ago
get GC across the entire CDS !
#look at GC across the entire CDS. gffread -x - -g | \ seqtk comp - | \ awk -v OFS="\t" '{ print $1, "0", $2, ($4 + $5) / $2 }'1389 days ago
- #GffRead: GFF/GTF utility providing format...:~$ conda install -c bioconda gffread Collecting package metad...added / updated specs: - gffread The following packag...64::_libgcc_mutex-0.1-main gffread bioconda/linux...NV) jitendra@Bathymodiolus:~$ gffread -w cds.fa -g ed.clean.fas...
1199 days ago
Install Install Gffcompare on Ubuntu / Linux
#Gffcompare is a program that is used to pe...operations on general feature format (GFF) and general transfer format...tp://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.9.8.Linux_x86_64.tar...# make symlink ln -s ~/workspace/bin/gffcompare-0.9.8.Linux_x86_64/gff...819 days ago
Identify genome-wide synteny with LASTZ alignment
...for both genomes and chromosomes. RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_rice.fa AAChr1.txt RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for...513 days ago
