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 …
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 …
Joined SPARQLthon held at DBCLS Mishima. This was 70th SPARQLthon.
After the intensive development of AOE system at BH18.7, we continued that work in this SPARQLthon.
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 …
Joined SPARQLthon held at DBCLS Kashiwa. This was 69th SPARQLthon.
We discussed a development of DBCLS SRA and AOE for this fiscal year.
How to get GEO metadata from NCBI was examined for sustainable retrieval system for AOE.
When we want to join two files by a same key into one file, we can use join command. We can join lines by a first column value of tab-delimited files.
join -j 1 file1 file2
Indeed, join command itself is very useful, default output is not tab-delimited text, but …
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 …
Joined SPARQLthon held at DBCLS Kashiwa. This was 68th SPARQLthon.
Updated version of AOE, which use Apache Solr as a back-end, officially released on this week, and we checked the web interface of AOE. It tentatively includes meta-data from NCBI Gene Expression Omnibus (GEO), which was taken from SRA/BioProject …
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 …