Skip to content

Instantly share code, notes, and snippets.

View antonkulaga's full-sized avatar

Anton Kulaga antonkulaga

109 followers · 85 following
View GitHub Profile
@antonkulaga
antonkulaga / gist:fdbd6a1ef43a0f188c55
Last active August 29, 2015 14:18
transcriptome assembly with Scythe-Sickle-Bowtie-Tophat-Stringtie-Cuffdiff
#NOTE: all actions are done with three samples, that have names: 3,4 and 9
###IMPROVING FASTQ###
#deleting illumina adapters by https://github.com/vsbuffalo/scythe
./sickle se -f /home/uploader/flies/assembly5/3_cleaned.fastq -t sanger /home/uploader/flies/assembly5/3.fastq
./sickle se -f /home/uploader/flies/assembly5/4_cleaned.fastq -t sanger /home/uploader/flies/assembly5/4.fastq
./sickle se -f /home/uploader/flies/assembly5/9_cleaned.fastq -t sanger /home/uploader/flies/assembly5/9.fastq
#triming fastq by https://github.com/najoshi/sickle
@antonkulaga
antonkulaga / gist:d0c76a2cd6e6de55b9af
Last active August 29, 2015 14:18
transcriptome assembly with Scythe-Sickle-Hisat-Stringtie-Ballgrown
###IMPROVING FASTQ (note: apply the same to all your fastq files) ###
#deleting illumina adapters by https://github.com/vsbuffalo/scythe
./sickle se -f /home/uploader/flies/assembly4/3_cleaned.fastq -t sanger /home/uploader/flies/assembly4/3.fastq
#triming fastq by https://github.com/najoshi/sickle
sickle se -f /home/uploader/flies/assembly4/3_cleaned.fastq -t sanger -o /home/uploader/flies/assembly4/3.fastq -q 25
### Hisat http://ccb.jhu.edu/software/hisat/manual.shtml ###
@antonkulaga
antonkulaga / gist:8586aa6b7f2ef47be670
Created April 2, 2015 17:44
FASTQ cleanup
java -jar ./trimmomatic-0.33.jar SE -threads 2 -phred33 /home/antonkulaga/data/raw/flies/fastq/3_TTAGGC_L003_R1_001.fastq /home/antonkulaga/data/raw/flies/cleanup/3_trm.fastq ILLUMINACLIP:/opt/trimmomatic/adapters/TruSeq2-SE.fa:2:30:10 SLIDINGWINDOW:4:25
@antonkulaga
antonkulaga / gist:d549ac8baba14d8112bb
Created January 6, 2015 10:54
Alistair Johnson 12:52
// A root, aggregate project
lazy val rootModule = XRootModule(moduleName = "notests", defaultSettings = buildSettings)
lazy val root = rootModule.project(rootJvm, rootJs)
lazy val rootJvm = rootModule.jvmProject(rdfJvm, dbJvm, jena)
lazy val rootJs = rootModule.jsProject(rdfJs, dbJs)
// The RDF Module
type m = Modules#rdf
@antonkulaga
antonkulaga / gist:e6239bb7aeabef1e020e
Created September 23, 2014 23:10
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<title>Keyboard events do not work for inputs. I cannot type anything there=(</title>
</head>
<body>
<script src="../build/three.min.js"></script>
@antonkulaga
antonkulaga / gist:9820118
Last active August 29, 2015 13:57
package org.denigma.frontend.extensions
import scala.collection.immutable._
import rx._
import rx.ops._
//NOTE THIS CODE IS NOT TESTED YET
trait RxCollectionOps {
/**
@antonkulaga
antonkulaga / gist:5575690
Created May 14, 2013 13:04
Several widgets on one page
jQuery ->
params =
widget_margins: [10, 10]
widget_base_dimensions: [250, 250]
shift_larger_widgets_down: false
draggable:
items: ".gs_w:not(.dashboard_static)"
gridster = $(".gridster ul").gridster(params).data('gridster');
@antonkulaga
antonkulaga / gist:5532205
Created May 7, 2013 12:29
Vivagraph serialization bug
###
it is an extract from one of my classes.
Here a save a log of nodes to the graph but only first one is shown =(
###
@graph = Viva.Graph.graph()
params =
container: @get("node")
@renderer = Viva.Graph.View.renderer(@graph, params)
@renderer.run()
@antonkulaga
antonkulaga / gist:5506349
Created May 2, 2013 23:53
When I do gen-idea (with 1.4.0 version) I get """ scala: Output path /home/antonkulaga/denigma/gene-app/modules/gene-actors/project/target/idea-test-classes is shared between: Module 'gene-actors-build' tests, Module 'semantic-data-build' tests Output path /home/antonkulaga/denigma/gene-app/modules/gene-actors/project/target/idea-classes is shar…
import sbt._
import sbt.Keys._
/**
* this files is intended to build the main project
* it contains links to all dependencies that are needed
* */
object ApplicationBuild extends GeneActors {
@antonkulaga
antonkulaga / gist:5497894
Created May 1, 2013 19:58
Experiments with scala-graph JSON
package semantic.graph
import scala.Predef._
import scalax.collection.mutable.{Graph => MGraph}
import scalax.collection.GraphEdge._
import scalax.collection.edge._
import scalax.collection.mutable._
import scalax.collection.edge.Implicits._