In this tutorial, we will perform an integrated analysis of ATAC-seq and RNA-seq during mouse development. The original analysis was published in Zhang, 2019.

This tutorial requires following additional software:

• samtools
• MACS2
• bwa
• bedGraphToBigWig

Preparing input

We will download the data from the ENCODE portal. First add the IDs of files to the input.tsv, and associate each record with the ENCODE tag. We will download and analyze raw FASTQ file for ATAC-seq experiments. For RNA-seq experiments, post-processed gene quantifications are available to download. So we will use those as our input, Taiji is capable of analyzing the raw FASTQ for RNA-seq as well though. To indicate that the files are gene quantifications, add GeneQuant tags to those files.

input.tsv:

type	id	group	rep	path	tags
ATAC-seq	ENCSR204ZTY	limb_E15.5	1	ENCFF629FRA,ENCFF222KJL	ENCODE
ATAC-seq	ENCSR204ZTY	limb_E15.5	2	ENCFF488EFS,ENCFF917DTZ	ENCODE
ATAC-seq	ENCSR150RMQ	embryonic facial prominence_E11.5	2	ENCFF741MLW,ENCFF460ETY	ENCODE
ATAC-seq	ENCSR150RMQ	embryonic facial prominence_E11.5	1	ENCFF667CEX,ENCFF165UKX	ENCODE
ATAC-seq	ENCSR358MOW	embryonic facial prominence_E13.5	2	ENCFF104GCO,ENCFF737HFT	ENCODE
ATAC-seq	ENCSR358MOW	embryonic facial prominence_E13.5	1	ENCFF166ANK,ENCFF512CMK	ENCODE
ATAC-seq	ENCSR983JWA	neural tube_E15.5	1	ENCFF847BCI,ENCFF608AWT	ENCODE
ATAC-seq	ENCSR983JWA	neural tube_E15.5	2	ENCFF551SAG,ENCFF166QOA	ENCODE
ATAC-seq	ENCSR623GSD	hindbrain_E16.5	1	ENCFF568THX,ENCFF196ILN	ENCODE
ATAC-seq	ENCSR623GSD	hindbrain_E16.5	2	ENCFF950API,ENCFF946KOT	ENCODE
ATAC-seq	ENCSR088UYE	hindbrain_E12.5	1	ENCFF954MPR,ENCFF824PVC	ENCODE
ATAC-seq	ENCSR088UYE	hindbrain_E12.5	2	ENCFF199WNL,ENCFF968KUR	ENCODE
ATAC-seq	ENCSR618HDK	stomach_E14.5	2	ENCFF395TZD,ENCFF395IGM	ENCODE
ATAC-seq	ENCSR618HDK	stomach_E14.5	1	ENCFF699GSF,ENCFF944CWK	ENCODE
ATAC-seq	ENCSR961SMM	intestine_E15.5	2	ENCFF867QVP,ENCFF771QNR	ENCODE
ATAC-seq	ENCSR961SMM	intestine_E15.5	1	ENCFF674OOP,ENCFF775MXU	ENCODE
ATAC-seq	ENCSR261ICG	embryonic facial prominence_E15.5	1	ENCFF724ZGT,ENCFF312YEC	ENCODE
ATAC-seq	ENCSR261ICG	embryonic facial prominence_E15.5	2	ENCFF139WZE,ENCFF322LEO	ENCODE
ATAC-seq	ENCSR154BXN	midbrain_E12.5	1	ENCFF680STO,ENCFF476NYE	ENCODE
ATAC-seq	ENCSR154BXN	midbrain_E12.5	2	ENCFF194BBQ,ENCFF867CGI	ENCODE
ATAC-seq	ENCSR903GMO	forebrain_E13.5	1	ENCFF401VUV,ENCFF898NRO	ENCODE
ATAC-seq	ENCSR903GMO	forebrain_E13.5	2	ENCFF721LGJ,ENCFF777UKE	ENCODE
ATAC-seq	ENCSR810HQR	forebrain_E14.5	1	ENCFF048MTG,ENCFF890LGM	ENCODE
ATAC-seq	ENCSR810HQR	forebrain_E14.5	2	ENCFF633MTW,ENCFF666DRJ	ENCODE
ATAC-seq	ENCSR836PUC	forebrain_E16.5	2	ENCFF058IAE,ENCFF765HUX	ENCODE
ATAC-seq	ENCSR836PUC	forebrain_E16.5	1	ENCFF776GDQ,ENCFF588XZG	ENCODE
ATAC-seq	ENCSR211OCS	midbrain_P0	2	ENCFF713VTW,ENCFF166GCN	ENCODE
ATAC-seq	ENCSR211OCS	midbrain_P0	1	ENCFF470CPP,ENCFF073BZO	ENCODE
ATAC-seq	ENCSR310MLB	forebrain_P0	2	ENCFF197GTC,ENCFF209GGJ	ENCODE
ATAC-seq	ENCSR310MLB	forebrain_P0	1	ENCFF296GZG,ENCFF664RZO	ENCODE
ATAC-seq	ENCSR363SKQ	stomach_E16.5	1	ENCFF310DVL,ENCFF545MGJ	ENCODE
ATAC-seq	ENCSR363SKQ	stomach_E16.5	2	ENCFF836EJZ,ENCFF528WNO	ENCODE
ATAC-seq	ENCSR377YDY	limb_E11.5	1	ENCFF156CTY,ENCFF507XBJ	ENCODE
ATAC-seq	ENCSR377YDY	limb_E11.5	2	ENCFF332GCF,ENCFF672BYU	ENCODE
ATAC-seq	ENCSR551WBK	limb_E12.5	1	ENCFF698GFS,ENCFF110KAU	ENCODE
ATAC-seq	ENCSR551WBK	limb_E12.5	2	ENCFF637TUL,ENCFF283VKJ	ENCODE
ATAC-seq	ENCSR700QBR	neural tube_E14.5	2	ENCFF726JSJ,ENCFF461GHH	ENCODE
ATAC-seq	ENCSR700QBR	neural tube_E14.5	1	ENCFF111RFS,ENCFF945IYI	ENCODE
ATAC-seq	ENCSR312LQX	hindbrain_P0	2	ENCFF971XEA,ENCFF215WAD	ENCODE
ATAC-seq	ENCSR312LQX	hindbrain_P0	1	ENCFF547YID,ENCFF131VHT	ENCODE
ATAC-seq	ENCSR559FAJ	forebrain_E12.5	1	ENCFF413XTH,ENCFF119TXW	ENCODE
ATAC-seq	ENCSR559FAJ	forebrain_E12.5	2	ENCFF199UBT,ENCFF171APM	ENCODE
ATAC-seq	ENCSR302LIV	liver_E12.5	2	ENCFF772GVP,ENCFF987EVS	ENCODE
ATAC-seq	ENCSR302LIV	liver_E12.5	1	ENCFF409BPW,ENCFF016UWL	ENCODE
ATAC-seq	ENCSR876SYO	embryonic facial prominence_E14.5	2	ENCFF185IWQ,ENCFF050LTK	ENCODE
ATAC-seq	ENCSR876SYO	embryonic facial prominence_E14.5	1	ENCFF369BHN,ENCFF043JPE	ENCODE
ATAC-seq	ENCSR597BGP	stomach_P0	1	ENCFF756RRU,ENCFF907CZS	ENCODE
ATAC-seq	ENCSR597BGP	stomach_P0	2	ENCFF550FMX,ENCFF601QOX	ENCODE
ATAC-seq	ENCSR966ORC	intestine_E16.5	2	ENCFF278MAA,ENCFF898FIK	ENCODE
ATAC-seq	ENCSR966ORC	intestine_E16.5	1	ENCFF880CTO,ENCFF896RTV	ENCODE
ATAC-seq	ENCSR102NGD	lung_P0	1	ENCFF705BQG,ENCFF269YOD	ENCODE
ATAC-seq	ENCSR102NGD	lung_P0	2	ENCFF370OFA,ENCFF150BVC	ENCODE
ATAC-seq	ENCSR552ABC	heart_E13.5	1	ENCFF100SXY,ENCFF064NKM	ENCODE
ATAC-seq	ENCSR552ABC	heart_E13.5	2	ENCFF406EUS,ENCFF559NSG	ENCODE
ATAC-seq	ENCSR603MWL	heart_E15.5	2	ENCFF385WYM,ENCFF051GLX	ENCODE
ATAC-seq	ENCSR603MWL	heart_E15.5	1	ENCFF829XFO,ENCFF694SPD	ENCODE
ATAC-seq	ENCSR335VJW	lung_E14.5	2	ENCFF204EVA,ENCFF437GNH	ENCODE
ATAC-seq	ENCSR335VJW	lung_E14.5	1	ENCFF979DGG,ENCFF244BWB	ENCODE
ATAC-seq	ENCSR819QOJ	midbrain_E13.5	2	ENCFF667HBE,ENCFF574MEU	ENCODE
ATAC-seq	ENCSR819QOJ	midbrain_E13.5	1	ENCFF659NJR,ENCFF703JZE	ENCODE
ATAC-seq	ENCSR668EIA	lung_E15.5	1	ENCFF507MHY,ENCFF217WJG	ENCODE
ATAC-seq	ENCSR668EIA	lung_E15.5	2	ENCFF159YPF,ENCFF940GZL	ENCODE
ATAC-seq	ENCSR798FDL	hindbrain_E14.5	2	ENCFF868CEL,ENCFF266VLC	ENCODE
ATAC-seq	ENCSR798FDL	hindbrain_E14.5	1	ENCFF673MIM,ENCFF657XRO	ENCODE
ATAC-seq	ENCSR652CNN	heart_E12.5	2	ENCFF719RSO,ENCFF086MTT	ENCODE
ATAC-seq	ENCSR652CNN	heart_E12.5	1	ENCFF377YCK,ENCFF982JWB	ENCODE
ATAC-seq	ENCSR150EOO	intestine_E14.5	1	ENCFF642UHQ,ENCFF188JXF	ENCODE
ATAC-seq	ENCSR150EOO	intestine_E14.5	2	ENCFF593JRX,ENCFF243SQC	ENCODE
ATAC-seq	ENCSR732OTZ	kidney_E16.5	1	ENCFF413HET,ENCFF021GRI	ENCODE
ATAC-seq	ENCSR732OTZ	kidney_E16.5	2	ENCFF573ZOR,ENCFF326PPN	ENCODE
ATAC-seq	ENCSR785NEL	liver_E11.5	1	ENCFF288CVJ,ENCFF888ZZV	ENCODE
ATAC-seq	ENCSR785NEL	liver_E11.5	2	ENCFF883SEZ,ENCFF035OMK	ENCODE
ATAC-seq	ENCSR068YGC	heart_E14.5	1	ENCFF826YDW,ENCFF258GFE	ENCODE
ATAC-seq	ENCSR068YGC	heart_E14.5	2	ENCFF753WMG,ENCFF031SEH	ENCODE
ATAC-seq	ENCSR976LWP	forebrain_E15.5	2	ENCFF248PXW,ENCFF825UHO	ENCODE
ATAC-seq	ENCSR976LWP	forebrain_E15.5	1	ENCFF906VXU,ENCFF500SXI	ENCODE
ATAC-seq	ENCSR273UFV	forebrain_E11.5	1	ENCFF419LDW,ENCFF963YIU	ENCODE
ATAC-seq	ENCSR273UFV	forebrain_E11.5	2	ENCFF083TDB,ENCFF680UAR	ENCODE
ATAC-seq	ENCSR662KNY	hindbrain_E15.5	2	ENCFF213OUA,ENCFF709CLT	ENCODE
ATAC-seq	ENCSR662KNY	hindbrain_E15.5	1	ENCFF761JHA,ENCFF181OVJ	ENCODE
ATAC-seq	ENCSR460BUL	limb_E14.5	1	ENCFF672EYN,ENCFF981BBK	ENCODE
ATAC-seq	ENCSR460BUL	limb_E14.5	2	ENCFF948NPO,ENCFF634JLT	ENCODE
ATAC-seq	ENCSR896XIN	limb_E13.5	1	ENCFF508LJX,ENCFF103PCA	ENCODE
ATAC-seq	ENCSR896XIN	limb_E13.5	2	ENCFF732HZX,ENCFF506NVN	ENCODE
ATAC-seq	ENCSR384JBF	midbrain_E14.5	1	ENCFF769SYG,ENCFF948TDP	ENCODE
ATAC-seq	ENCSR384JBF	midbrain_E14.5	2	ENCFF227ATX,ENCFF307UMX	ENCODE
ATAC-seq	ENCSR217NOA	neural tube_E13.5	1	ENCFF336EQO,ENCFF308AMG	ENCODE
ATAC-seq	ENCSR217NOA	neural tube_E13.5	2	ENCFF843JWW,ENCFF577DNF	ENCODE
ATAC-seq	ENCSR371KFW	heart_E16.5	1	ENCFF416BZL,ENCFF473REG	ENCODE
ATAC-seq	ENCSR371KFW	heart_E16.5	2	ENCFF304CCF,ENCFF778FWU	ENCODE
ATAC-seq	ENCSR032HKE	liver_E14.5	1	ENCFF159HYY,ENCFF911HQX	ENCODE
ATAC-seq	ENCSR032HKE	liver_E14.5	2	ENCFF618OJP,ENCFF863FZP	ENCODE
ATAC-seq	ENCSR079GOY	intestine_P0	2	ENCFF169QUZ,ENCFF742CFJ	ENCODE
ATAC-seq	ENCSR079GOY	intestine_P0	1	ENCFF039HAM,ENCFF780FQW	ENCODE
ATAC-seq	ENCSR820ACB	heart_E11.5	1	ENCFF279LMU,ENCFF820PVO	ENCODE
ATAC-seq	ENCSR820ACB	heart_E11.5	2	ENCFF823XXU,ENCFF518FYP	ENCODE
ATAC-seq	ENCSR023QZX	kidney_E15.5	2	ENCFF395EDU,ENCFF100YMT	ENCODE
ATAC-seq	ENCSR023QZX	kidney_E15.5	1	ENCFF340WOK,ENCFF117TPW	ENCODE
ATAC-seq	ENCSR096JCC	midbrain_E16.5	2	ENCFF518FPU,ENCFF754FRO	ENCODE
ATAC-seq	ENCSR096JCC	midbrain_E16.5	1	ENCFF458XRA,ENCFF882GWB	ENCODE
ATAC-seq	ENCSR468GUI	midbrain_E15.5	2	ENCFF267LVT,ENCFF347QTV	ENCODE
ATAC-seq	ENCSR468GUI	midbrain_E15.5	1	ENCFF187YXW,ENCFF865ZYW	ENCODE
ATAC-seq	ENCSR758IRM	kidney_E14.5	2	ENCFF802JNF,ENCFF576WIS	ENCODE
ATAC-seq	ENCSR758IRM	kidney_E14.5	1	ENCFF958YUR,ENCFF504EBV	ENCODE
ATAC-seq	ENCSR451NAE	heart_P0	2	ENCFF913PMS,ENCFF483MKX	ENCODE
ATAC-seq	ENCSR451NAE	heart_P0	1	ENCFF655OFT,ENCFF999SZR	ENCODE
ATAC-seq	ENCSR282YTE	neural tube_E11.5	2	ENCFF187AQG,ENCFF994STU	ENCODE
ATAC-seq	ENCSR282YTE	neural tube_E11.5	1	ENCFF529IDC,ENCFF149EJI	ENCODE
ATAC-seq	ENCSR690VOH	neural tube_E12.5	1	ENCFF226GOU,ENCFF444RRA	ENCODE
ATAC-seq	ENCSR690VOH	neural tube_E12.5	2	ENCFF927BDD,ENCFF303PPN	ENCODE
ATAC-seq	ENCSR382RUC	midbrain_E11.5	1	ENCFF747ZCB,ENCFF236CXJ	ENCODE
ATAC-seq	ENCSR382RUC	midbrain_E11.5	2	ENCFF315TMY,ENCFF752YLN	ENCODE
ATAC-seq	ENCSR343TXK	liver_E13.5	2	ENCFF360MVK,ENCFF443PRW	ENCODE
ATAC-seq	ENCSR343TXK	liver_E13.5	1	ENCFF382CMV,ENCFF688ZFD	ENCODE
ATAC-seq	ENCSR465PYP	liver_E15.5	1	ENCFF329VCX,ENCFF290ZBP	ENCODE
ATAC-seq	ENCSR465PYP	liver_E15.5	2	ENCFF341HRL,ENCFF489XAT	ENCODE
ATAC-seq	ENCSR486XAS	stomach_E15.5	1	ENCFF997AUJ,ENCFF033YBG	ENCODE
ATAC-seq	ENCSR486XAS	stomach_E15.5	2	ENCFF211VPG,ENCFF442KCP	ENCODE
ATAC-seq	ENCSR609OHJ	liver_P0	1	ENCFF599TJR,ENCFF176IZG	ENCODE
ATAC-seq	ENCSR609OHJ	liver_P0	2	ENCFF957VLH,ENCFF999IJT	ENCODE
ATAC-seq	ENCSR389CLN	kidney_P0	1	ENCFF171RXE,ENCFF144HIW	ENCODE
ATAC-seq	ENCSR389CLN	kidney_P0	2	ENCFF763EEB,ENCFF765QFH	ENCODE
ATAC-seq	ENCSR176BYZ	hindbrain_E13.5	2	ENCFF331IGF,ENCFF409GTD	ENCODE
ATAC-seq	ENCSR176BYZ	hindbrain_E13.5	1	ENCFF071AXB,ENCFF628CBN	ENCODE
ATAC-seq	ENCSR031HDN	embryonic facial prominence_E12.5	1	ENCFF265RFZ,ENCFF547OQI	ENCODE
ATAC-seq	ENCSR031HDN	embryonic facial prominence_E12.5	2	ENCFF492KHX,ENCFF459CPD	ENCODE
ATAC-seq	ENCSR012YAB	hindbrain_E11.5	2	ENCFF753PKM,ENCFF635ZQL	ENCODE
ATAC-seq	ENCSR012YAB	hindbrain_E11.5	1	ENCFF058UWO,ENCFF163UHB	ENCODE
ATAC-seq	ENCSR627OCR	lung_E16.5	1	ENCFF577XAL,ENCFF224TAO	ENCODE
ATAC-seq	ENCSR627OCR	lung_E16.5	2	ENCFF872IZI,ENCFF427HTC	ENCODE
ATAC-seq	ENCSR255XTC	liver_E16.5	2	ENCFF702NAP,ENCFF243ROW	ENCODE
ATAC-seq	ENCSR255XTC	liver_E16.5	1	ENCFF894ZND,ENCFF788EQO	ENCODE
RNA-seq	ENCSR691OPQ	heart_E11.5	1	ENCFF226IWR	ENCODE,GeneQuant
RNA-seq	ENCSR691OPQ	heart_E11.5	2	ENCFF540EJL	ENCODE,GeneQuant
RNA-seq	ENCSR908JWT	midbrain_E12.5	2	ENCFF887JHQ	ENCODE,GeneQuant
RNA-seq	ENCSR908JWT	midbrain_E12.5	1	ENCFF399CQH	ENCODE,GeneQuant
RNA-seq	ENCSR420QTO	hindbrain_E12.5	2	ENCFF242PFZ	ENCODE,GeneQuant
RNA-seq	ENCSR420QTO	hindbrain_E12.5	1	ENCFF983XDK	ENCODE,GeneQuant
RNA-seq	ENCSR504GEG	kidney_E14.5	1	ENCFF499WRT	ENCODE,GeneQuant
RNA-seq	ENCSR504GEG	kidney_E14.5	2	ENCFF413OJO	ENCODE,GeneQuant
RNA-seq	ENCSR851HEC	embryonic facial prominence_E12.5	1	ENCFF594CEM	ENCODE,GeneQuant
RNA-seq	ENCSR851HEC	embryonic facial prominence_E12.5	2	ENCFF742JLO	ENCODE,GeneQuant
RNA-seq	ENCSR401BSG	hindbrain_E15.5	1	ENCFF395LAH	ENCODE,GeneQuant
RNA-seq	ENCSR401BSG	hindbrain_E15.5	2	ENCFF338ZXD	ENCODE,GeneQuant
RNA-seq	ENCSR448MXQ	liver_E13.5	1	ENCFF615ZTQ	ENCODE,GeneQuant
RNA-seq	ENCSR448MXQ	liver_E13.5	2	ENCFF336VTP	ENCODE,GeneQuant
RNA-seq	ENCSR466KZY	stomach_E16.5	1	ENCFF288JNN	ENCODE,GeneQuant
RNA-seq	ENCSR466KZY	stomach_E16.5	2	ENCFF052DOQ	ENCODE,GeneQuant
RNA-seq	ENCSR367ZPZ	midbrain_E16.5	1	ENCFF918YFP	ENCODE,GeneQuant
RNA-seq	ENCSR367ZPZ	midbrain_E16.5	2	ENCFF052VJO	ENCODE,GeneQuant
RNA-seq	ENCSR290RRR	stomach_E14.5	1	ENCFF050PAT	ENCODE,GeneQuant
RNA-seq	ENCSR290RRR	stomach_E14.5	2	ENCFF691EQW	ENCODE,GeneQuant
RNA-seq	ENCSR823VEE	embryonic facial prominence_E14.5	1	ENCFF924CMS	ENCODE,GeneQuant
RNA-seq	ENCSR823VEE	embryonic facial prominence_E14.5	2	ENCFF370UDF	ENCODE,GeneQuant
RNA-seq	ENCSR370SFB	intestine_E15.5	1	ENCFF052THP	ENCODE,GeneQuant
RNA-seq	ENCSR370SFB	intestine_E15.5	2	ENCFF114YCL	ENCODE,GeneQuant
RNA-seq	ENCSR830IVQ	limb_E15.5	1	ENCFF532ZDE	ENCODE,GeneQuant
RNA-seq	ENCSR830IVQ	limb_E15.5	2	ENCFF003DBZ	ENCODE,GeneQuant
RNA-seq	ENCSR537GNQ	kidney_E16.5	1	ENCFF752QKG	ENCODE,GeneQuant
RNA-seq	ENCSR537GNQ	kidney_E16.5	2	ENCFF143OJZ	ENCODE,GeneQuant
RNA-seq	ENCSR347SQR	limb_E13.5	1	ENCFF358WYS	ENCODE,GeneQuant
RNA-seq	ENCSR347SQR	limb_E13.5	2	ENCFF634AUL	ENCODE,GeneQuant
RNA-seq	ENCSR020DGG	heart_E16.5	1	ENCFF415JBI	ENCODE,GeneQuant
RNA-seq	ENCSR020DGG	heart_E16.5	2	ENCFF871IGQ	ENCODE,GeneQuant
RNA-seq	ENCSR284YKY	heart_E13.5	1	ENCFF242GMD	ENCODE,GeneQuant
RNA-seq	ENCSR284YKY	heart_E13.5	2	ENCFF976CYB	ENCODE,GeneQuant
RNA-seq	ENCSR597UZW	heart_E15.5	1	ENCFF440PWB	ENCODE,GeneQuant
RNA-seq	ENCSR597UZW	heart_E15.5	2	ENCFF219PVC	ENCODE,GeneQuant
RNA-seq	ENCSR538WYL	embryonic facial prominence_E13.5	1	ENCFF132NQU	ENCODE,GeneQuant
RNA-seq	ENCSR538WYL	embryonic facial prominence_E13.5	2	ENCFF867TKM	ENCODE,GeneQuant
RNA-seq	ENCSR062VTB	kidney_E15.5	1	ENCFF700YRC	ENCODE,GeneQuant
RNA-seq	ENCSR062VTB	kidney_E15.5	2	ENCFF347HOK	ENCODE,GeneQuant
RNA-seq	ENCSR457RRW	lung_E15.5	1	ENCFF718PJC	ENCODE,GeneQuant
RNA-seq	ENCSR457RRW	lung_E15.5	2	ENCFF996EMC	ENCODE,GeneQuant
RNA-seq	ENCSR727FHP	heart_E14.5	1	ENCFF111IGW	ENCODE,GeneQuant
RNA-seq	ENCSR727FHP	heart_E14.5	2	ENCFF540BJT	ENCODE,GeneQuant
RNA-seq	ENCSR750YSX	limb_E12.5	1	ENCFF879FXB	ENCODE,GeneQuant
RNA-seq	ENCSR750YSX	limb_E12.5	2	ENCFF470WZZ	ENCODE,GeneQuant
RNA-seq	ENCSR611PTP	liver_E15.5	1	ENCFF740SXP	ENCODE,GeneQuant
RNA-seq	ENCSR611PTP	liver_E15.5	2	ENCFF504YJB	ENCODE,GeneQuant
RNA-seq	ENCSR921PRX	hindbrain_E13.5	1	ENCFF131WIM	ENCODE,GeneQuant
RNA-seq	ENCSR921PRX	hindbrain_E13.5	2	ENCFF604LWF	ENCODE,GeneQuant
RNA-seq	ENCSR992WBR	lung_E16.5	1	ENCFF538RNR	ENCODE,GeneQuant
RNA-seq	ENCSR992WBR	lung_E16.5	2	ENCFF365SND	ENCODE,GeneQuant
RNA-seq	ENCSR080EVZ	forebrain_E16.5	1	ENCFF590FAC	ENCODE,GeneQuant
RNA-seq	ENCSR080EVZ	forebrain_E16.5	2	ENCFF484AOO	ENCODE,GeneQuant
RNA-seq	ENCSR285WZV	hindbrain_E16.5	1	ENCFF211ELX	ENCODE,GeneQuant
RNA-seq	ENCSR285WZV	hindbrain_E16.5	2	ENCFF830YBR	ENCODE,GeneQuant
RNA-seq	ENCSR932TRU	intestine_E14.5	1	ENCFF959OHE	ENCODE,GeneQuant
RNA-seq	ENCSR932TRU	intestine_E14.5	2	ENCFF228SAS	ENCODE,GeneQuant
RNA-seq	ENCSR647QBV	forebrain_E12.5	1	ENCFF804FTJ	ENCODE,GeneQuant
RNA-seq	ENCSR647QBV	forebrain_E12.5	2	ENCFF601JPN	ENCODE,GeneQuant
RNA-seq	ENCSR752RGN	forebrain_E15.5	1	ENCFF763GXJ	ENCODE,GeneQuant
RNA-seq	ENCSR752RGN	forebrain_E15.5	2	ENCFF340XFQ	ENCODE,GeneQuant
RNA-seq	ENCSR792RJV	midbrain_E13.5	1	ENCFF422BJI	ENCODE,GeneQuant
RNA-seq	ENCSR792RJV	midbrain_E13.5	2	ENCFF196WAD	ENCODE,GeneQuant
RNA-seq	ENCSR115TWD	neural tube_E13.5	1	ENCFF502BTV	ENCODE,GeneQuant
RNA-seq	ENCSR115TWD	neural tube_E13.5	2	ENCFF049EIV	ENCODE,GeneQuant
RNA-seq	ENCSR557RMA	midbrain_E15.5	1	ENCFF706XGJ	ENCODE,GeneQuant
RNA-seq	ENCSR557RMA	midbrain_E15.5	2	ENCFF835FSF	ENCODE,GeneQuant
RNA-seq	ENCSR648YEP	liver_E12.5	1	ENCFF746VZM	ENCODE,GeneQuant
RNA-seq	ENCSR648YEP	liver_E12.5	2	ENCFF468PFF	ENCODE,GeneQuant
RNA-seq	ENCSR508GWZ	neural tube_E12.5	1	ENCFF353TCZ	ENCODE,GeneQuant
RNA-seq	ENCSR508GWZ	neural tube_E12.5	2	ENCFF224SRI	ENCODE,GeneQuant
RNA-seq	ENCSR848GST	intestine_E16.5	1	ENCFF443JRH	ENCODE,GeneQuant
RNA-seq	ENCSR848GST	intestine_E16.5	2	ENCFF278PAQ	ENCODE,GeneQuant
RNA-seq	ENCSR906YQZ	stomach_E15.5	1	ENCFF972NMO	ENCODE,GeneQuant
RNA-seq	ENCSR906YQZ	stomach_E15.5	2	ENCFF355MOU	ENCODE,GeneQuant
RNA-seq	ENCSR636CWO	embryonic facial prominence_E15.5	1	ENCFF369TLJ	ENCODE,GeneQuant
RNA-seq	ENCSR636CWO	embryonic facial prominence_E15.5	2	ENCFF536XKZ	ENCODE,GeneQuant
RNA-seq	ENCSR004XCU	neural tube_E15.5	1	ENCFF037GWJ	ENCODE,GeneQuant
RNA-seq	ENCSR004XCU	neural tube_E15.5	2	ENCFF365DLM	ENCODE,GeneQuant
RNA-seq	ENCSR970EWM	forebrain_E13.5	1	ENCFF567AFL	ENCODE,GeneQuant
RNA-seq	ENCSR970EWM	forebrain_E13.5	2	ENCFF227HKF	ENCODE,GeneQuant
RNA-seq	ENCSR826HIQ	liver_E16.5	1	ENCFF759PUL	ENCODE,GeneQuant
RNA-seq	ENCSR826HIQ	liver_E16.5	2	ENCFF512KYX	ENCODE,GeneQuant
RNA-seq	ENCSR928OXI	neural tube_E14.5	1	ENCFF513HAL	ENCODE,GeneQuant
RNA-seq	ENCSR928OXI	neural tube_E14.5	2	ENCFF967SJG	ENCODE,GeneQuant
RNA-seq	ENCSR284AMY	liver_E11.5	1	ENCFF954EHG	ENCODE,GeneQuant
RNA-seq	ENCSR284AMY	liver_E11.5	2	ENCFF523MEO	ENCODE,GeneQuant
RNA-seq	ENCSR331XCE	intestine_P0	1	ENCFF485CJB	ENCODE,GeneQuant
RNA-seq	ENCSR331XCE	intestine_P0	2	ENCFF795XBQ	ENCODE,GeneQuant
RNA-seq	ENCSR160IIN	forebrain_E11.5	1	ENCFF465SNB	ENCODE,GeneQuant
RNA-seq	ENCSR160IIN	forebrain_E11.5	2	ENCFF976OLT	ENCODE,GeneQuant
RNA-seq	ENCSR719NAJ	midbrain_P0	1	ENCFF210MWH	ENCODE,GeneQuant
RNA-seq	ENCSR719NAJ	midbrain_P0	2	ENCFF793WMU	ENCODE,GeneQuant
RNA-seq	ENCSR096STK	liver_P0	1	ENCFF875HIA	ENCODE,GeneQuant
RNA-seq	ENCSR096STK	liver_P0	2	ENCFF143HKK	ENCODE,GeneQuant
RNA-seq	ENCSR337FYI	neural tube_E11.5	1	ENCFF375JDR	ENCODE,GeneQuant
RNA-seq	ENCSR337FYI	neural tube_E11.5	2	ENCFF298WHK	ENCODE,GeneQuant
RNA-seq	ENCSR982MRY	lung_P0	1	ENCFF990GIB	ENCODE,GeneQuant
RNA-seq	ENCSR982MRY	lung_P0	2	ENCFF658LQM	ENCODE,GeneQuant
RNA-seq	ENCSR307BCA	midbrain_E11.5	1	ENCFF359ZOA	ENCODE,GeneQuant
RNA-seq	ENCSR307BCA	midbrain_E11.5	2	ENCFF971KZC	ENCODE,GeneQuant
RNA-seq	ENCSR559TRB	hindbrain_E14.5	1	ENCFF206KRT	ENCODE,GeneQuant
RNA-seq	ENCSR559TRB	hindbrain_E14.5	2	ENCFF741FZD	ENCODE,GeneQuant
RNA-seq	ENCSR362AIZ	forebrain_P0	1	ENCFF918QNL	ENCODE,GeneQuant
RNA-seq	ENCSR362AIZ	forebrain_P0	2	ENCFF895JXR	ENCODE,GeneQuant
RNA-seq	ENCSR526SEX	heart_P0	1	ENCFF817KPY	ENCODE,GeneQuant
RNA-seq	ENCSR526SEX	heart_P0	2	ENCFF155GNG	ENCODE,GeneQuant
RNA-seq	ENCSR216NEG	limb_E14.5	1	ENCFF677BPV	ENCODE,GeneQuant
RNA-seq	ENCSR216NEG	limb_E14.5	2	ENCFF794QMH	ENCODE,GeneQuant
RNA-seq	ENCSR848HOX	embryonic facial prominence_E11.5	1	ENCFF772UWT	ENCODE,GeneQuant
RNA-seq	ENCSR848HOX	embryonic facial prominence_E11.5	2	ENCFF262TXH	ENCODE,GeneQuant
RNA-seq	ENCSR760TOE	hindbrain_E11.5	1	ENCFF750FTK	ENCODE,GeneQuant
RNA-seq	ENCSR760TOE	hindbrain_E11.5	2	ENCFF109HTF	ENCODE,GeneQuant
RNA-seq	ENCSR185LWM	forebrain_E14.5	1	ENCFF745ZJF	ENCODE,GeneQuant
RNA-seq	ENCSR185LWM	forebrain_E14.5	2	ENCFF816CVP	ENCODE,GeneQuant
RNA-seq	ENCSR178GUS	stomach_P0	1	ENCFF517XLT	ENCODE,GeneQuant
RNA-seq	ENCSR178GUS	stomach_P0	2	ENCFF434XNZ	ENCODE,GeneQuant
RNA-seq	ENCSR017JEG	hindbrain_P0	1	ENCFF798MSP	ENCODE,GeneQuant
RNA-seq	ENCSR017JEG	hindbrain_P0	2	ENCFF861GUP	ENCODE,GeneQuant
RNA-seq	ENCSR867YNV	liver_E14.5	1	ENCFF432ZGG	ENCODE,GeneQuant
RNA-seq	ENCSR867YNV	liver_E14.5	2	ENCFF572OPZ	ENCODE,GeneQuant
RNA-seq	ENCSR173PJN	kidney_P0	1	ENCFF905HUL	ENCODE,GeneQuant
RNA-seq	ENCSR173PJN	kidney_P0	2	ENCFF783LVC	ENCODE,GeneQuant
RNA-seq	ENCSR541XZK	limb_E11.5	1	ENCFF195JHC	ENCODE,GeneQuant
RNA-seq	ENCSR541XZK	limb_E11.5	2	ENCFF457ZGF	ENCODE,GeneQuant
RNA-seq	ENCSR039ADS	lung_E14.5	1	ENCFF872ABP	ENCODE,GeneQuant
RNA-seq	ENCSR039ADS	lung_E14.5	2	ENCFF226ILJ	ENCODE,GeneQuant
RNA-seq	ENCSR343YLB	midbrain_E14.5	1	ENCFF453GZG	ENCODE,GeneQuant
RNA-seq	ENCSR343YLB	midbrain_E14.5	2	ENCFF870YWY	ENCODE,GeneQuant
RNA-seq	ENCSR150CUE	heart_E12.5	2	ENCFF343NNZ	ENCODE,GeneQuant
RNA-seq	ENCSR150CUE	heart_E12.5	1	ENCFF345NEQ	ENCODE,GeneQuant

config.yml:

input: "input.tsv"
output_dir: "output/"
assembly: "mm10"

Running the analysis

This is a large dataset containing 264 experiments. It is not feasible to analyze such a large dataset on a personal desktop. Nowadays large-scale computing usually happens in the cloud. So in this tutorial I will show you how to use Taiji in a HPC cluster.

First you need to have an access to a HPC cluster that supports slurm or PBS like workload manager. Now, put following lines in your config.yml file:

submit_params: "-q home -l walltime=10:00:00"
submit_command: "qsub"
submit_cpu_format: "-l nodes=1:ppn=%d"
submit_memory_format: "-l mem=%dG

This configuration works for The Triton Shared Computing Cluster (TSCC) at UCSD. You may need to make adjustment for your local environment.

The submission parameters of individual step are configurable as well:

resource:
  RNA_Align:
    parameter: "-q home -l walltime=24:00:00"
    memory: 50

  ATAC_Align:
    memory: 10

Once you have your config.yml file ready, run the analysis using:

taiji run --config config.yml --cloud

Results

Here are some of the QC metrics:

Number of Reads

TSS enrichment

Fragment size distribution

Taiji combines motif scanning, network inference and the PageRank algorithm to rank TFs. This result will be saved in the GeneRank.tsv file. There is also a GeneRank.html file that you can visualize.

TF Ranking scores (showing 639 TFs across 66 tissues)