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mRNA-seq (NGS) nrog rau cov genome siv

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mRNA-seq (NGS) nrog rau cov genome siv

RNA-seq yog ib qho cuab yeej txheem thoob plaws kev tshawb fawb txog lub neej thiab qoob loo, txuas qhov sib txawv ntawm cov genomes thiab proteomes. Nws lub zog nyob hauv kev tshawb pom cov ntawv sau tshiab thiab ntsuas lawv cov lus qhia hauv ib qho kev sim. Nws siv dav rau kev tshawb fawb sib piv transcriptomic, qhia txog cov noob caj noob ces cuam tshuam nrog ntau yam cwj pwm lossis phenotypes, zoo li sib piv cov mutants rau cov tsiaj qus lossis qhia cov lus qhia gene hauv qab cov xwm txheej tshwj xeeb. BMKCloud mRNA (Reference) APP koom ua ke kev ntsuas kev qhia tawm, kev tshuaj xyuas kev qhia tawm sib txawv (DEG), thiab kev tshuaj xyuas cov qauv sib lawv liag rau hauv mRNA-seq (NGS) bioinformatics pipeline thiab sib xyaw cov zog ntawm cov software zoo sib xws, ua kom yooj yim thiab yooj yim rau cov neeg siv. Cov neeg siv tuaj yeem upload lawv cov ntaub ntawv RNA-seq rau huab, qhov twg App muab cov kev daws teeb meem bioinformatic ib zaug xwb. Tsis tas li ntawd, nws muab qhov tseem ceeb rau cov neeg siv khoom, muab cov haujlwm tus kheej uas haum rau cov neeg siv cov kev xav tau tshwj xeeb. Cov neeg siv tuaj yeem teeb tsa cov kev cai thiab xa cov dej num ntawm lawv tus kheej, tshawb xyuas daim ntawv qhia sib tham, saib cov ntaub ntawv / daim duab thiab ua tiav cov ntaub ntawv tshawb nrhiav, xws li: kev xaiv cov noob caj noob ces, kev sib sau ua ke, kev kos duab, thiab lwm yam.

Cov txiaj ntsig ntawm kev sim
Kev khawb cov ntaub ntawv
Yuav tsum tau xa khoom tuaj
Kev tshuaj xyuas tseem ceeb
Siv ua piv txwv
Cov txiaj ntsig ntawm kev sim

Kev khawb cov ntaub ntawv

Yuav tsum tau xa khoom tuaj

Platform:Illumina, MGI
Txoj Kev Npaj:RNA-Seq
Kev teeb tsa: Pared, huv-cov ntaub ntawv.
Hom tsev qiv ntawv:fr-unstranded, fr-firststrand lossis fr-secondstrand
Nyeem ntev:150 bp
Hom ntaub ntawv:*.fastq, *.fq, *.fastq.gz lossis *.fq.gz. Lub kaw lus yuavcia li txuas cov ntaub ntawv .fastq raws li lawv cov npe ntaub ntawv,piv txwv li *_1.fastq ua ke nrog *._2.fastq.
Tus naj npawb ntawm cov qauv:Tsis muaj kev txwv rau tus lejntawm cov qauv kuaj, tab sis lub sijhawm tshuaj xyuas yuav nce ntxiv raws li tus lej ntawmcov qauv loj hlob.
Cov Ntaub Ntawv Pom Zoo:6G ib qho qauv

Kev tshuaj xyuas tseem ceeb
Cov cuab yeej tseem ceeb ntawm kev tshuaj xyuas thiab bioinformatic ntawm mRNA-seq (Siv)Cov kav dej yog raws li nram no:
1. Kev Tswj Xyuas Zoo ntawm Cov Ntaub Ntawv Raw:
• Tshem tawm cov kab ke tsis zoo, cov kab ke adapter,thiab lwm yam;
•Cov cuab yeej: cov kav dej tsim tawm hauv tsev;
2. Kev sib phim ntawm cov ntaub ntawv rau ib qho genome siv:
•Kev sib phim cov nyeem nrog lub algorithm splice-aware tawm tsamgenome siv rau.
•Cov Cuab Yeej:HISAT2, samtools
3. Kev tshuaj xyuas qhov zoo ntawm tsev qiv ntawv:
•Ntxig kev tsom xam qhov ntev, kev tsom xam qhov sib lawv liag, thiab lwm yam;
•Cov Cuab Yeej:samtools;
4. Kev tshuaj xyuas cov qauv ntawm cov kab ke:
•Kev tshuaj xyuas lwm txoj kev sib txuas, kev txhim kho cov qauv noob caj noob ces,kev kwv yees cov noob caj noob ces tshiab, thiab lwm yam;
•Cov Cuab Yeej:Txoj Hlua Khi, gffcompare, GATK,Pob Zeb Diamond, InterProScan, thiabHMMER.
5. Kev tshuaj xyuas qhov sib txawv ntawm cov lus qhia:
•Kev tshuaj xyuas DEG, kev tshuaj xyuas kev sib raug zoo, kev ua haujlwmkev nplua nuj;
Cov txiaj ntsig pom tau ntau yam;
RnrogSEGseq, DESeq2, ggplot2, DEXSeq
Siv ua piv txwv
1. Kim, Daehwan et al. “Kev sib phim ntawm cov genome raws li daim duab thiabkev tshuaj ntsuam xyuas nrog HISAT2 thiab HISAT-genotype.XwmKev siv tshuab biotechnology37 (2019): 907 - 915.
2. McKenna, Aaron et al. “Cov Cuab Yeej Siv Los Tshawb Fawb Txog Genome: aMapReduce lub moj khaum rau kev tshuaj xyuas DNA tiam tom ntejcov ntaub ntawv txheeb xyuas.Kev tshawb nrhiav txog genome209 (2010): 1297-303.
3. Li, Heng et al. “Daim Ntawv Qhia Txog Kev Sib Tshuam/Daim Ntawv Qhia thiabSAM cov cuab yeej.Kev tshawb fawb txog bioinformatics25 (2009): 2078 - 2079.
4. Perțea, Mihaela et al. “StringTie pab txhim khokev tsim kho dua tshiab ntawm cov ntawv sau los ntawm RNA-seq nyeem.XwmKev siv tshuab biotechnology33 (2015): 290-295.
5. Kev Hlub, Michael I. thiab lwm tus. "Kev kwv yees ntawm kev hloov pauv ntawm qhov quav thiabkev sib kis rau cov ntaub ntawv RNA-seq nrog DESeq2.GenomeKev tshawb fawb txog tsiaj txhu15 (2014): n. nplooj ntawv.
6. Eddy, Sean R.. “Kev Tshawb Nrhiav Profile HMM Sai.”PLoS Kev suav lej Biology7 (2011): n. nplooj ntawv.

tau ib daim ntawv hais nqe

Sau koj cov lus ntawm no thiab xa tuaj rau peb

Xa koj cov lus rau peb: