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@inutano
inutano / ajacs51_inutano.md
Created December 5, 2014 05:41

DDBJパイプラインとGalaxyによるデータ解析

情報・システム研究機構
ライフサイエンス統合データベースセンター
大田達郎 [email protected]

prepared for AJACS岩手
December 5, 2014

@soh-i
soh-i / bamReader.scala
Created July 18, 2014 13:57
ScalaでBamファイルを読み込んでみる
import java.io.File
import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMFileWriter
import net.sf.samtools.SAMFileWriterFactory
import net.sf.samtools.SAMRecord
import net.sf.samtools.SAMRecordIterator
import net.sf.samtools.SAMFileReader.ValidationStringency
object BamReader {
@brentp
brentp / fq.split.py
Last active December 23, 2015 10:59
split a fastq file into evenly size random chunks.
"""
split a single fastq file in to random, non-overlapping subsets
arguments:
+ fastq file
+ number of splits
+ number of reps
e.g.:
python fq.split.py input.fastq 3 4
@mchirico
mchirico / gzipWriter.go
Created August 3, 2013 19:34
Example of writing a gzip file in go (golang). This appends data to the same file every time it is run. It is important to Flush() the data before closing the file.
/*
This is an example of a golang gzip writer program,
which appends data to a file.
*/
package main
@arq5x
arq5x / make-master-hmm.sh
Created July 18, 2012 20:19
For Gemini: Create a master ChromHMM track from the 9 distinct cell types.
echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \
> chromhmm-files.txt