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 …grep has various options.
I frequently use -v option to filter lines without the keyword.
grep -v human data.txt
where data.txt is a bunch of data to be greped.
We can filter out lines with keyword human.
Other example is to filter the lines which have a value …
It turned out that the command I regularly use to search a bunch of data is not known to others.
I frequently use fgrep to grep against a list of keywords (i.e. IDs).
fgrep -f keywords.txt data.txt
where keywords.txt contains a list of keywords ('one keyword …
Joined SPARQLthon held at DBCLS Mishima. This was 78th SPARQLthon.
First, I tried to execute SPARQL from UNIX command line for the integration of unfamiliar data. According to the SPARQL book (p145), I could make it.
# command line execution of SPARQL
% curl -F query=@hoge.rq -H "Accept: application/sparql-results …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 joined BioHackathon2018 held at Matsue. I also joined Common Workflow Language (CWL) Workshop Tokyo 2018 held at Shibuya prior to the hackathon, and learned a little bit about CWL.
I have other tasks (update searchability of All of gene expression (AOE)) to be discussed in the hackathon, but it …
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 …When we submit relatively large entries to DDBJ, we use Mass Submission System (MSS). We will use MSS for submitting transcriptome sequence assembly (TSA) to DDBJ.
After extracting the list of IDs from header lines of FASTA by command like
% perl -nle 'print $1 if(/^\>(\S+)/) hoge.fasta > id.txt' …
Identifiers (IDs) in public databases often contain version information.
For example, .16 in ENSG00000100644.16 from Ensembl and .1 in NM_001243084.1 from RefSeq.
Such version information can be an obstacle to join entries from different databases.
So, version information should be trimmed before joining.
The file that contains such …