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searchindex.js
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Search.setIndex({docnames:["Intro/Installation_Guide_SATAY_Analysis_Software","Intro/data-analysis-workflow","Intro/satay_analysis_notes","Introduction","MysT_Notebooks","from-reads-to-essential-genes","gene_reads","statistics_perchromosome_Compare","statistics_pergene","transposonmapping_satay"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.index":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,sphinx:56},filenames:["Intro/Installation_Guide_SATAY_Analysis_Software.md","Intro/data-analysis-workflow.md","Intro/satay_analysis_notes.md","Introduction.md","MysT_Notebooks.md","from-reads-to-essential-genes.ipynb","gene_reads.md","statistics_perchromosome_Compare.md","statistics_pergene.md","transposonmapping_satay.md"],objects:{},objnames:{},objtypes:{},terms:{"0x7fb98f651e50":5,"0x7fb99c389dd0":5,"0x7fb99d21d1d0":5,"123fastq":1,"123ng":0,"16bp":1,"1_20150113":1,"1gb":1,"20analysi":1,"20modul":1,"25th":[6,7],"2_compar":7,"2mer":1,"432x288":5,"500mb":1,"50bp":1,"50gb":0,"50th":6,"545bp":2,"6bp":2,"75bp":[1,2],"75th":[6,7],"76bp":1,"76m":2,"case":[1,2,8],"class":5,"default":[0,1,3,4,9],"final":[1,5,6,7],"float":[5,6],"function":[1,2,4,5,6,7,8],"import":[0,1,2,5,6,7,8],"int":[1,6,7,8,9],"long":[1,2,3],"m\u00e4hler":1,"new":[0,1,2,3,7],"public":3,"return":5,"short":[1,2],"static":[0,1],"true":[3,5,6,7,8,9],"try":[1,8],"var":[1,5],"while":[1,4,6],ADDED:6,ADE:2,AND:[6,8,9],ARE:[6,8],Added:9,And:[2,4],Are:2,Axes:5,BUT:9,But:[1,2,8],CDS:[1,2],FOR:[6,7,8,9],For:[0,1,2,3,4,5,6,7,9],IDE:0,ITS:6,Ins:1,LTS:0,NGS:1,NOT:[6,7,8],ONE:8,ONES:6,One:1,POS:[1,2],THAT:8,THE:[6,7,8,9],THEIR:8,THERE:6,That:5,The:[0,1,3,4,5,9],Then:1,There:[0,1,2,4],These:[0,1,2,8],USING:6,Use:[0,1,3,5],Using:[1,2],VMs:1,WITH:[6,8,9],With:[1,2,5],__author__:9,__call__:5,__date:9,__file__:[5,6,7,8,9],__main__:9,__name__:9,__version__:9,_amin:5,_base:5,_build:3,_classif:5,_datacompar:7,_draw_list_compositing_imag:5,_method:5,_novalu:5,_peressenti:9,_peressential_insert:9,_pergen:[8,9],_pergene_insert:9,_size:5,_sum:5,_tninsert:6,_trim:1,_warn_prf:5,aac1:9,abcd:1,abil:2,abl:[0,1,2],about:[1,2,4,8,9],abov:[0,1,4,5],abs:[6,7,9],abs_gff_fil:6,abs_path_data_insert:5,abs_path_data_read:5,absolut:[1,2,5,7,9],abspath:[6,9],accept:[1,2,3],access:[0,1,3],accolad:1,accompani:1,accord:[1,2,5,9],account:6,accumul:1,accur:1,accuraci:5,acid:8,action:3,activ:3,actual:[0,1,2,6,8],adapt:[0,1],adapters_original_backup:1,add:[0,1,3,4,6,7,9],added:[0,1,2],adding:[1,4],addit:[0,1,6,7,9],addition:2,addus:0,ade2:2,ade5:8,adenin:2,adjac:5,advanc:0,advantag:1,advic:[0,1],advis:1,affect:1,after:[0,1,2,3,4,5,7],again:[0,1,3],against:2,agent:3,agre:[2,8],agtcn:1,agtcnagtcn:1,aim:2,albican:[1,8],algorithm:[1,2,9],alia:6,alias:[6,8,9],aliases_designation_dict:9,aliass:8,align:[0,6,9],alignmentfil:9,all:[0,1,4,5,7,9],alloc:0,allow:[0,1,2,4],along:6,alpha:[5,6,8],alreadi:[1,2,7,9],also:[0,1,2,4,5,6,7,9],alter:1,altern:[0,1,2],although:[1,2],alwai:[1,2,4],ambigu:2,amino:8,among:1,amount:[0,1,2,6,8,9],ampersand:1,amplif:1,anaconda:3,analys:[2,3,6,8,9],analysi:[0,2,3,6,8,9],analyz:[1,2,8],ani:[0,1,2,5,6,7,8],annot:[2,6,8,9],anoth:[0,1,2,4],anymor:[0,2,9],anywai:1,anywher:1,apart:8,app:0,appear:[1,2,6],append:[5,6,7,8,9],appli:[0,1,5],applic:0,approach:2,approxim:1,apt:0,arang:5,area:[6,7],arg5:8,arg:5,argsort:9,argument:[1,9],argv:9,around:[1,2],arrai:[1,5,6,9],arrayexpress:1,arter:[1,6,7,8],artist:5,asarrai:[5,6],ascend:1,ascii:[1,2],asciit:2,ask:0,aspect:1,assembl:2,assess:1,assign:2,associ:1,assum:[1,9],assur:5,astyp:5,atgt:2,attach:4,attent:2,atur:3,auto:[0,1,3],autodetect:1,automat:[0,1,2,4,6,7,8],avail:[0,1,4,9],averag:[1,5,6,8],avg:5,avg_start_po:9,awai:2,awar:2,ax1:8,ax2:8,axes:5,axessubplot:5,axi:[5,6,9],axisgrid:5,axvlin:[6,8],babraham:[0,1],back:1,backend:5,backend_bas:5,background:[1,2],backup:[1,3],backward:2,bacteria:2,bad:1,bai:[1,9],bam:[0,6,7,9],bam_arg:9,bam_pergen:[1,8],bamfil:9,baminfo:1,bamread:1,bar:[2,6],barplot:6,barren:1,base:[0,1,3,8,9],basenam:[1,9],basepair:[1,2,6,7,8,9],basepairtech:1,bash:[0,1,3],basic:[1,8],bat:1,batch:0,bbmap:[0,1],bbox:[5,6],bbox_extra_artist:5,bbox_inch:5,bbtool:0,becaus:[0,1,2,6],becom:[1,2,6],bed:[1,6,7,9],bed_fil:[6,7],bed_file_count:7,bedfil:9,bedtool:1,beek:9,been:[2,9],befor:[0,1,2,8],begin:[1,3,6,7],behavior:5,behind:2,being:5,bellow:[3,5],belong:[1,2],below:[0,1,2,7],bem1:6,bem3:2,benoit:[6,8],besid:[1,2],best:1,better:[1,2,6],between:[0,1,2,4,5,6,7,8,9],bia:1,bidirect:0,bigger:[1,2],bil1:8,bin:[0,1,8],bin_width:6,binari:[1,2],bind:2,binder:5,bins_read:8,bins_tn:8,bio:[0,1],bioinfo:1,bioinformat:[0,1,6],biomap:1,bionanosci:9,bit:[0,1],bitwis:2,black:[5,6],block:[2,4],blue:[0,1,5,6,8],blueish:1,bodi:2,bold:[1,6],boldfac:1,book:[2,4],boon:1,both:[0,1,2,4,6,8],bound:5,bowtie2:1,box:1,boxplot:5,boxstyl:6,bp_between:7,bp_between_tn_insert:[6,7],bp_between_tn_insertions_chr_dic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Software installation guide for whole genome sequencing and transposon mapping\u201d","<span class=\"section-number\">2. </span>Data analysis steps","<span class=\"section-number\">1. </span>All what you need to know from SATAY","To reproduce an example of Jupyter book, and you are a Windows user:","<span class=\"section-number\">3. </span>Notebooks written entirely in markdown","<span class=\"section-number\">4. </span>From reads and insertions to essentiality prediction using a Regression Model","<span class=\"section-number\">1. </span>Gene reads script","<span class=\"section-number\">3. </span>Comparison of the statistics per chromosome","<span class=\"section-number\">2. </span>Statistics per gene","<span class=\"section-number\">1. </span>Python Translation of the Matlab code from Kornmann 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