Installing Platypus on Ubuntu !
...MiB | 1.11 MiB/s, done. Resolving deltas: 100% (729/729), don...r (3.6.5-3) ... Selecting previously unselected package libpy...You should consider upgrading via the 'pip install --upgrade p...install platypus-variant Solving environment: done ## Pac...2032 days ago
2017 days ago
CollectGcBiasMetrics.jar will generate a GC bias plot for each contig
samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam...2017 days ago
Setting up falconUnzip conda environments for genome assembly !
...onda create -n denovo_asm Solving environment: done ## Package Pl...conda install pb-assembly Solving environment: done ## Pac...# PacBio(R) tools distributed via Bioconda are: pre-release ve...# PacBio(R) tools distributed via Bioconda are: pre-release ve...2003 days ago
1847 days ago
Samtools commands for bioinformatician !
...: output file name samtools view -b -S -o sal_sej.bam sal_sej.sam ### viewing bam files (view command)...c) by flag specified samtool view -c -f 4 sal_sej.bam ##...potential variants bcftools view -c -v sal_vars.bcf > sal_va...nvert BAM to FASTA: samtools view filename.bam | awk '{OFS="\...1616 days ago
Perl script to remove duplicated lines !
...ext_line$/"; print $_ if $_ ne $next_line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__ apple apple plum vinegar apple banana banana...1573 days ago
Bash script to alignment of short reads against reference genome !
...fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b - >SRR1770413.raw.bam s...e the second mate. #conversion to BAM: samtools view -b - --- this reads SAM fro...fastq.gz SRR341549_2.fastq.gz \ | samtools view -b - >SRR341549.raw.minimap...1572 days ago
Bash commandline to install Anaconda !
...r to continue the installation process, please review the license agreement. Pl...une-0.8.4-py37h7b6447c_0 ... installing: mkl-service-1.1.2-py37he904b0f_5 ... i...ng: jupyter_core-4.4.0-py37_0 ... installing: navigator-updater-0.2.1-py37_0 ......1568 days ago
Bash command to install Miniconda !
...conda3-latest-Linux-x86_64.sh Resolving repo.anaconda.com... 104.16...1785000 (68M) [application/x-sh] Saving to: `Miniconda3-latest-Linu...the installation process, please review the license agreement. Pl...Solving environment: done ## Pac...1568 days ago