As I had to map assembled reads to the genomic sequence, I used BLAT (the BLAST-like Alignment Tool) for that purpose. BLAT was so fast for landing reads to genomic sequence, but it can be slow if reads are so many. I thought it would be so nice to have …
Joined SPARQLthon held at DBCLS Kashiwa. This was 67th SPARQLthon.
Discussed the development of two search systems (DBCLS SRA and AOE) and the integration of these. The specification will be fixed after the coming INSDC meeting of this year at NCBI.
I tried to add contents to how to make …
Joining two files by key in the first column of files can be easily done by using UNIX command below.
join -j 1 file1.txt file2.txt
This is very useful command, but the output is space-delimited by default. In order to get the output by tab-delimited, following option for …
In order to extract a set of sequence from FASTA-formatted file (both in nucleotides and peptides), several commands can be used to do so.
In recent years, I regularly use blastdbcmd in NCBI BLAST suite. To run this command, the file must be indexed by makeblastdb with the option below …
When I want to count the number of redundant words in a file (hoge.txt), I have used simple Perl code like this(count.pl).
1 2 3 4 5 6 7 8 | #!/usr/bin/perl
while(<>) {
my($word) = split;
$num{$word}++;
}
foreach (sort keys %num) {
print "$_\t$num … |
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 …
Paper in collaboration with Dr. Tanimoto at Hiroshima University in Japan was published.
Differentiated Embryo Chondrocyte plays a crucial role in DNA damage response via transcriptional regulation under hypoxic conditions DOI:
10.1371/journal.pone.0192136
This study contained my work on the collective intelligence of hypoxic transcriptome from public …
Joined SPARQLthon held at DBCLS Mishima located at National Institute of Genetics. This was 65th SPARQLthon.
Discussed the development of search system for public high-throughput sequencing data at Sequence Read Archive (SRA).
Last summer, our work on the use of FANTOM5 data was published in Scientific Data.
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes
This article was included in FANTOM5 collection. It was a great pleasure to be published together with FANTOM5 data …
When I want to extract data by numeric value in other column, Perl in awk mode might be useful. It is often the case that I forget the option for that in Perl, so I took a note this time.
perl -anle 'print "$F[0]\t$F[3]" if ($F …