rmihael’s gists

rmihael / gist:01b594b3374c11eecc1a

Last active August 29, 2015 14:19

Flies differential expression

	#cat << EOT > polyAT.fa
	#>polyA/1
	#AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
	#>polyT/1
	#TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
	#EOT
	#trimmomatic SE -phred33 raw/3_TTAGGC_L003_R1_001.fastq filtered/3_TTAGGC_L003_R1_001.fastq HEADCROP:15 ILLUMINACLIP:/usr/local/share/trimmomatic/adapters/TruSeq3-SE.fa:2:30:10 ILLUMINACLIP:polyAT.fa:2:30:10 TRAILING:30 MINLEN:75
	bowtie2-build dmel-all-chromosome-r6.04.fasta dmel.bowtie.index
	ln -s dmel-all-chromosome-r6.04.fasta dmel.bowtie.index.fa
	tophat2 -p 8 --GTF dmel-all-r6.04.gtf --transcriptome-index dmel.transcriptome.tophat dmel.bowtie.index

rmihael / gist:4ebc76e587db3ee4f2b8

Last active August 29, 2015 14:06

RNA-Seq differential expression

	bowtie2-build dmel-all-chromosome-r6.03.fasta dmel.bowtie.index
	ln -s dmel-all-chromosome-r6.03.fasta dmel.bowtie.index.fa
	tophat2 -p 4 --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat dmel.bowtie.index
	tophat2 -p 4 --no-novel-juncs --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat -o 3_TTAGGC_L003_R1_001.tophat dmel.bowtie.index 3_TTAGGC_L003_R1_001.fastq.gz
	tophat2 -p 4 --no-novel-juncs --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat -o 4_TGACCA_L003_R1_001.tophat dmel.bowtie.index 4_TGACCA_L003_R1_001.fastq.gz
	tophat2 -p 4 --no-novel-juncs --GTF dmel-all-r6.03.gff --transcriptome-index dmel.transcriptome.tophat -o 9_GATCAG_L003_R1_001.tophat dmel.bowtie.index 9_GATCAG_L003_R1_001.fastq.gz
	samtools view -h 3_TTAGGC_L003_R1_001.tophat/accepted_hits.bam > 3_TTAGGC_L003_R1_001.tophat/accepted_hits.sam
	samtools view -h 4_TGACCA_L003_R1_001.tophat/accepted_hits.bam > 4_TGACCA_L003_R1_001.tophat/accepted_hits.sam
	samtools view -h 9_GATCAG_L00

rmihael / gist:ca7d95ecbcefa9bc6bc7

Created September 18, 2014 21:47

Так работает. Фокус в том, что в данных flybase вообще нет аннотаций по хромосомам. По крайней мере я не нашёл ни одного такого продукта. В данных Ensembl есть, но "annotations are imported from FlyBase release 5.46 (FB2012_04, dated 6 July 2012)". Надо найти способ аннотировать хромосомами данные flybase.

	wget ftp://ftp.ensembl.org/pub/release-76/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP5.dna.toplevel.fa.gz
	wget ftp://ftp.ensembl.org/pub/release-76/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP5.76.gtf.gz
	gunzip Drosophila_melanogaster.BDGP5.76.gtf.gz Drosophila_melanogaster.BDGP5.dna.toplevel.fa.gz
	snapr index Drosophila_melanogaster.BDGP5.dna.toplevel.fa index
	snapr transcriptome Drosophila_melanogaster.BDGP5.76.gtf Drosophila_melanogaster.BDGP5.dna.toplevel.fa transcriptome -bSpace

rmihael / UpperBound.scala

Created September 25, 2013 06:20

	trait GenericCache[Key, Value] {
	def retrieve(key: Key): Value
	def insert(key: Key, value: Value): Unit
	}

	case class FastCache[Key, Value]() extends GenericCache[Key, Value] {
	private var m = Map[Key, Value]() //excuse mutability for illustration purposes

	def retrieve(key: Key): Value = m(key)