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.1151 days ago
3021 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...2921 days ago
2118 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...3088 days ago
2877 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.gz1377 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";} $...1377 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
1774 days ago
Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies ...Tags: Liftoff, accurate, tool, maps, annotations, GFF, GTF, assemblies
1416 days ago
1532 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...2304 days ago