Written by bonohu in DBCLS on 金 24 8月 2018.

Joined SPARQLthon held at DBCLS Kashiwa. This was 71st SPARQLthon.

Try to update AOE data for the latest one, but there was some trouble in this process. There might be unexpected characters in the contents of original data. It was because names in the header line were conflicted. After the …

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Local reverse complement

Written by bonohu in shell on 日 29 7月 2018.

To get reverse complement for specific DNA string is frequently needed in molecular biology. There were some web interface to do that, but it is not secure. Calculating reverse complement locally is ideal solution for that issue.

In the search of an example code with practical usefulness in GitHub, I …

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Moving to cleanly installed High Sierra

Written by bonohu in shell on 木 12 7月 2018.

As there was a mechanical trouble in my main machine, MacBookPro, I am moving to new MacBookPro with cleanly installed High Sierra (10.13.6). Below is a log for my future replication...

First of all, default shell was changed with chsh command to /bin/zsh.

After installing Homebrew, coreutils …

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Trinity will not run

Written by bonohu in rnaseq on 水 06 6月 2018.

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 …

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Written by bonohu in rnaseq on 金 18 5月 2018.

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 …

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Written by bonohu in rnaseq on 木 17 5月 2018.

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TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.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 …

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