Running salmon via CWL

Written by bonohu in rnaseq on 金 28 6月 2019.

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.

19 …

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Running ikra

Written by bonohu in rnaseq on 火 21 5月 2019.

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 …

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grep -v

Written by bonohu in shell on 金 19 4月 2019.

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 …

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Written by bonohu in shell on 木 18 4月 2019.

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 …

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Written by bonohu in DBCLS on 金 29 3月 2019.

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 …

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Written by bonohu in rnaseq on 土 02 2月 2019.

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 older fastq-dump tool.

So I tested the speed from my home.

  1. Just specify a run ID of SRA.
# Just fasterq-dump …

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Written by bonohu in rnaseq on 火 06 11月 2018.

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://"))'
# Run …

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Removing version information in IDs

Written by bonohu in shell on 金 31 8月 2018.

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 …

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