fastqc - A quality control tool for high throughput sequence data SPAdes - An assembly toolkit containing various assembly pipelines bwa - The BWA read mapper samtools - Tools for dealing with SAM, BAM and CRAM files bamtools - C++ API and command-line toolkit for working with BAM data bed...
It is possible that the Homebrew installation will ask you to install Xcode or the Command Line Tools for Xcode. Whether it does and which it suggests would be dependent on your OS version and the versions of the C and C++ compilers installed on your system. According to the Homebrew instal...
First I trim_galore the reads, and then I make a bismark_genome_preparation on those sequences and run bismark on them, however no a a single read mapped on them. Is this the correct way of doing that? Here are the code: trim_galore -q 25 --phred33 --fastqc --illumina --rrbs ...
libhdhomerun protobuf@2.6 zanata-client faas-cli libical proxychains-ng zebra fabric libmagic pspg zero-install fakeroot libomp pulseaudio zimg fastqc libosmium pushpin znc ==> Deleted Formulae artifactory-cli-go boot2docker-completion ghc@8.0 gpg-agent wry boot2docker dirmngr gnupg@2.0 node@4 ...
docker run --rm --name fastqc_albot -u="$(id -u):$(id -g)" -w="/data/" -v ~/workshop-janssen/data/:/data quay.io/biocontainers/fastqc:0.11.9--0 /bin/bash -c "fastqc WT*.fq.gz" the shell expansion part is not always necessary but depends on where you are in your fol...
Widely accepted external tools for this step are, for example, FastQC, Cutadapt, and Trimommatic. In the next step, these clean sRNA reads have to be mapped on the reference database. For the specifics of isomiR identification, and the study of the sequence variant set that a particular ...