Public Databases for Bioinformatics !
...HM.bam as we as the GENCODE annotation v29 from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.1137 days ago
3006 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...000 organizations have invested in CLC Accepts VCF files from 1000 Genomes Project Accepts downloaded tracks from dbSNP Also accepts: FASTA, GFF/GTF/GVF, BED, Wiggle, Cosmic, UCS...2906 days ago
2104 days ago
ArrayGen Next Generation Genome Browser Coming Soon !!!
...data analysis. It is platform independent and much simpler to use. The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can b...3074 days ago
2862 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1363 days ago
Bash script to extract intronic fragments !
...the gene and exonic coordinates; #by subtracting the exonic regions from the genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $...1363 days ago
Tags: Genome Browser, Organism, Plant, Animal, Bacteria, fungi, Genome Sequence, DNA, Sequencing, Annotation, SNP, gff, gtf, gff3, vcf, bed
3912 days ago
GffCompare: Program for processing GTF/GFF files
The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).Tags: GffCompare, Program, processing, GTF, GFF
1759 days ago
1518 days ago
Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
...econdary index .gmidxsec is also generated. -d, --reads STR Path to the reads file. -o, --out STR Path to the output file that will be generated. --gtf STR Path to a General Transfe...2290 days ago