BOL: Results for "gtf"

Results for "gtf"

- Jit@jit.aber
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
- Jitendra Narayan@admin
CrossMap
...hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed t...
3006 days ago
+9 more Bookmarks

- Jitendra Prajapati@jprajapati81
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
- EagleEye@santhilalsubhash
Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass, Strand) Raw
...sp; Information: This script converts EnsEMBL GTF (Ex: https://gist.github...cfb803e07900a2baefbb6534f1299fd30cb57a29/sample.GTF) file to annotation table for...de0af1a39f0005c4ce7321c5ae57fc8b4a14c7f4/sample.GTF_enst_annotation.txt)2) Gene w...
2104 days ago
+1 more Top-level pages

- Abhimanyu Singh@abhimanyu
To print the matching pattern line perl -ne '/pattern/ && print' infile.gtf #Perloneliner #Tipsoftheday
3867 days ago
- Jit@jit.aber
Comparing Ensembl GTF and cDNA https://www.r-bloggers.com/comparing-ensembl-gtf-and-cdna-2/ #Comparing #Ensembl #GTF #cDNA
1552 days ago

- ArrayGen Technologies@arraygen
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
- Gudiya Pal@gudiya
Genome Workbench 2.10.7
...sues in GVF import Fixed BLAST Search tool against NCBI databases not working Fixed tblastn (protein BLAST) not working in standalone mode Fixed GTF export failure...
2862 days ago

- BioStar@biostar
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.gz
1363 days ago
- BioStar@biostar
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
+3 more Bio-Scripts

- Jit@jit.aber
Comment on "ASCIIGenome: genome browser based on command line interface and designed for running from console terminals."
...p; GTF/GFF attribute to set the feat...
1518 days ago
- Jit@jit.aber
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