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...on-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose[sudo] password for urbe: Re...lib-data python-mpmath python-nose python-numexpr python-numpy...xenial/universe amd64 python-nose all 1.3.7-1 [116 kB]Get:54...sly unselected package python-nose.Preparing to unpack .../pyt...2245 days ago
Creating conda environment for python2.7
...vironment: conda create --name myenv NOTE: Replace myenv wi...on that you are currently using, because you did not specify a version. To creat...ncy conflicts. To automatically install pip or another program every time a new...2245 days ago
Learning Python Programming - a bioinformatician perspective !
...e strings of characters (for example, strings of DNA bases and protein amino acid residues, which we as bi...cation development. Python is interpreted language so the program does not need to be compiled. Interpr...2238 days ago
Convert VCF to tab-deilimited table
Performed with GATK : java -Xmx8g -jar GenomeAnalysisTK.jar \ -T VariantsToTable \ -R reference.fa \ -V reference_genomes_GT.vcf \ -F CHROM -F POS -F REF -F ALT -GF GT \ -o reference_genomes_GT.table multiple_sample....2237 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
....bwasw.sam gsnap -A sam -d hs37m r1.fq r2.fq > r12.gsnap.sam novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo > r12.novo.sam smal...2237 days ago
Ancestral sequence reconstruction steps !
...sequence reconstruction (ASR) – also known as ancestral gene/sequ...that only started to be fulfilled in the post-genomic era. Thanks to the im..."http://www.datamonkey.org/" - turning to the amino acid seaview -> view prote...2234 days ago
Gap filling or Contigs extensions tools !
...s" or "Toward almost closed genomes with GapFiller". There are...used GAPresolution but it is not a very good software, it is...k at the IMAGE tool: http://genomebiology.com/2010/11/4/R41...a. Identify paired-end reads (not in C) for which one or both...2220 days ago
LINKS scaffolder bloomfilter setting !
...0: fatal error: ../BloomFilter.hpp: No such file or directory compi.../BloomFilter.hpp:141:59: warning: ignoring return value of ‘size_t f...eads (default -m 1 = yes, default = no, optional) ! DO NOT SET IF...-f WITH SAME -k VALUE IF YOU DO NOT SUPPLY A BLOOM FILTER, ONE W...2206 days ago
Understanding BLASTn output format 6 !
...mple gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabu... 2. sseqid subject (e.g., reference genome) sequence id 3. pid...ck operations (BTOP)staxids Subject Taxonomy ID(s), separated by a ';'ss...2194 days ago
List of non-commercial NGS genotype-calling software
...ccurate calling of SNPs and genotypes. Recently developed stat...uncertainty associated with genotype calling, and will especia...ncludes a single individual genotype caller (SOAPsnp) realSFS...s, which includes a SNP and genotype caller (Unifed Genotyper)...2151 days ago
