Bash script to alignment of short reads against reference genome !
...3_1.fastq.gz SRR1770413_2.fastq.gz --- this just specifies the base reference file name (bwa finds the indexes using this) and the input alignment files. The first file should contai...1559 days ago
Install Nucmer on Linux / Ubuntu
...mummer amd64 3.23+dfsg-3 [811 kB] Fetched 1,213 kB in 2s (672 kB/s) Selecting previously unselected package gawk. (Reading database ... 186076 files and directories currently ins...1550 days ago
Install python pip and numpy on Linux / Ubuntu
...y unselected package libexpat1-dev:amd64. (Reading database ... 186309 files and directories currently ins.../MitoHunter$ pip install numpy Collecting numpy Downloading https://files.pythonhosted.org/packages/3a/...1550 days ago
Install miniasm in Linux / Ubuntu
...4 minimap amd64 0.2-3 [26.6 kB] Fetched 55.8 kB in 1s (40.7 kB/s) Selecting previously unselected package miniasm. (Reading database ... 187073 files and directories currently ins...1550 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...ing whether we are cross compiling... no checking for suffix of object files... o checking whether we are...in/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/type...1550 days ago
To convert just one specific read group to fastq
...t selected.txt | parallel fastq-dump -O reads -X 1000 --split-files {} # Create a directory for bam files mkdir -p bam # Generate a...process is to extract reads, tagged with readgroups to paired files. samtools fastq -t -1 all1.f...1542 days ago
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Install python-numpy python-scipy python-matplotlib on Ubuntu !
...Selecting previously unselected package tk8.6-blt2.5. (Reading database ... 190390 files and directories currently ins...1541 days ago
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