If a transcriptome sequence set is available for the organism, salmon can be used for transcript quantification.
cwltool must be installed in advance by conda install cwltool or pip install cwltool.
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Tried to use ikra. SRR mode which directly fetches SRA file from NCBI worked fine, but FASTQ mode was failed after trimming with the error below. It seems that the file setting for salmon was incorrect.
Exception : [
The following errors were detected with the read files
======================================================
ERROR: file [fq/ERRxxxxxx_trimmed …I noticed the announcement in NCBI's sra-tools GitHub wiki
With release 2.9.1 of sra-tools we have finally made available the tool
fasterq-dump, a replacement for the much olderfastq-dumptool.
So I tested the speed from my home.
# Just fasterq-dump …I tried to use CellFishing written in Julia. It was my first time to use Julia, so I started from the installation of Julia with Homebrew.
# Install Julia
brew cask install julia
# Install CellFishing
julia -e 'using Pkg; Pkg.add(PackageSpec(url="git://github.com/bicycle1885/CellFishing.jl.git"))'
# Run …After some software updates, Trinity ended with error below.
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgomp.1.dylib
Referenced from: /usr/local/Cellar/trinity/2.5.1/util/..//Inchworm/bin/fastaToKmerCoverageStats Reason: image not found
I checked the file /usr/local/opt/gcc/lib/gcc …
After the execution of HISAT2, aligned reads can be assembled using StringTie.
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
The pipeline to process data by HISAT2 and StringTie is similar to that by TopHat and Cufflinks. Genome annotation file (GTF) can be used …
HISAT2 is a successor of TopHat.
TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.
Genome annotation file (GTF) is …
If assembled transcriptome sequence set and RNA-seq reads for that are available for an organism, we can align reads and estimate transcript abundance by running the script (align_and_estimate_abundance.pl) in the Trinity software package. When the Trinity package was installed using Homebrew, that script is installed in /usr/local/Cellar …
If a transcriptome sequence set is available for the organism, kallisto can be used for transcript quantification. The kallisto version I used was 0.43.1, which was previously installed using Homebrew by the command like brew install kallisto.
kallisto index -i index transcriptome.fa
kallisto quant -i index -o …Following instruction in sleuth official page,
sleuth was successfully install except there was a permission problem in my /usr/local.
I fixed that with a command, sudo chown -R bono /usr/local.