rmihael
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| #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
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| 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.
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| 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
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| 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) |