parallelized BLAT

Written by bonohu in misc on 火 01 5月 2018.

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 …

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Written by bonohu in DBCLS on 金 27 4月 2018.

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 …

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Join files by key

Written by bonohu in shell on 日 25 3月 2018.

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 …

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Retrieve a subset of sequence dataset

Written by bonohu in shell on 土 24 3月 2018.

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 …

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uniq -c option

Written by bonohu in shell on 金 23 3月 2018.

When I want to count the number of redundant words in a file (hoge.txt), I have used simple Perl code like this(

while(<>) {
        my($word) = split;
foreach (sort keys %num) {
        print "$_\t$num …

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Align and estimate abundance

Written by bonohu in rnaseq on 水 07 3月 2018.

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 ( in the Trinity software package. When the Trinity package was installed using Homebrew, that script is installed in /usr/local/Cellar …

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Perl in awk mode

Written by bonohu in shell on 月 05 2月 2018.

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 …

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