BOL: Results for "BED"

Results for "BED"

- Jit@jit.aber
Computer simulation of genetic mechanism !!
...ects/episimsimulator/files/ EvolSimulator A simulation test bed for hypotheses of genome evol...ForwSim The program given below is based on the algorithm described in Padhukasahasram et al. 200...
2969 days ago
- Rahul Nayak@rahul
Understanding liftOver !
...ber from one build to another (3) Convert both genome position and dbSNP rs number over different versions Run: liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed The outformat i...
2154 days ago

- Jit@jit.aber
Public Databases for Bioinformatics !
...p;https://www.encodeproject.org/files/ENCFF446WOD/@@download/ENCFF446WOD.bed.gz, https://www.encodepr...anford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz. The human genome version...
1133 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 d...
3003 days ago
+14 more Bookmarks

- Jit@jit.aber
List of generic simulation software/tools/resource with brief description and homepage !!!
...genomics. http://egglib.sourceforge.net/EvolSimulator A simulation test bed for hypotheses of genome evol...rch.shtmlForwSim The program given below is based on the algorithm described in Padhukasahasram et al. 200...
3731 days ago
- Surabhi Chaudhary@surabhi
Commercial and public next-gen-seq (NGS) software
...on Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. (C++) SISSRs - Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH....
3513 days ago
+2 more Top-level pages

- Jit@jit.aber
Get the fasta sequence of the coordinates http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #Bedtools
2609 days ago
- Jit@jit.aber
get the fasta genes using gff3 and genome.fa sequence: ~/Tools/bedtools2/bin/bedtools getfasta -fi vaga.fa -bed Adineta_vaga.v2.gff3 -fo Adineta_vaga_genes.fa
2295 days ago
+5 more Wire posts

- ArrayGen Technologies@arraygen
ArrayGen Next Generation Genome Browser Coming Soon !!!
...cing 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...
3070 days ago

- Surajeet@surajeet
The 2014 CeMM PhD Program
...heir research. Positions are offered by CeMM Faculty in June. Start of PhD Program: 1st October 2014 . Contact Binia Maria Günther, BEd BA Human Resources Manager...
3736 days ago

- Jit@jit.aber
Downloading GATK !
...-------- Intervals Manipulation: Tools that process genomic intervals in various formats BedToIntervalList (Picard) Converts a BED file to a Picard Interval Lis...
2069 days ago
- Jit@jit.aber
Install HTSLIB on Ubuntu !
...test/realn02_exp-e.sam htslib-1.9/test/realn02_exp.sam htslib-1.9/test/sam.c htslib-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/tab...
2013 days ago
+7 more Bio-Scripts

- Rahul Nayak@rahul
Comment on "Genome in a Bottle (GIAB) Consortium"
...e technologies to generate variant calls and regions for use in benchmarking and validating variant calling pipelines. Currently, benchmark VCF and BED files for small variants are...
1554 days ago
- Jit@jit.aber
Comment on "AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data"
...quencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. The input can be SAM, BAM, FASTA, BED files or Chromosome size file...
2131 days ago