Samtools commands for bioinformatician !
...-c sal_sej.bam ### sorting bam file by genome position samtools sort sal...ndex sal_sej_sorted.bam.bam ### identifying genome variants (mpileup command)...ted_bam.bam > /path/to/coverage_results.txt ### note: returns count of depth at...1658 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam sambam...1614 days ago
Bash commandline to install Anaconda !
...Do you accept the license terms? [yes|no] Please answer 'yes' or 'no':' >>> yes Anaconda3 wi...alling: six-1.12.0-py37_0 ... installing: snowballstemmer-1.2.1-py37_0 ......lling: networkx-2.2-py37_1 ... installing: nose-1.3.7-py37_2 ... installin...1610 days ago
Bash command to install Miniconda !
...ER to continue >>> ... ... ... Please answer 'yes' or 'no':' >>> yes Miniconda3 will now be installed into this locat...in/linux-64::tk-8.6.8-hbc83047_0 tqdm pkgs/main/noarch::tqdm-4.36.1-py_0 urll...1610 days ago
Bash command to install bwa, samtools, picard !
...pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre pkgs/main/linux-64::pcre-8.43-he6710b0_0 picard bioconda/noarch::picard-2.21.7-0 pixma...1610 days ago
Bash command to install GATK, Bedtools and SnpEff !
...2019.11.28-py38_0 gatk bioconda/noarch::gatk-3.8-7 pip...on-3.8.1-h0371630_1 r-assertthat pkgs/r/noarch::r-assertthat-0.2.1-r36h6...l be INSTALLED: snpeff bioconda/noarch::snpeff-4.3.1t-3 Pro...1610 days ago
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Perl script to delete the adjacent repeats !
...nt $string; #For more helps ... check out this #This bit of code will do the job: $string =~ s/(.)\1/$1/g #Alternatively, if you want to ignore case when comparing, you co...1605 days ago