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...2539 days ago
Plot custom gene density with R
library(karyoploteR) pp2266 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, "...2155 days ago
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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 }'1409 days ago
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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...839 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...533 days ago