I-mRNA-seq (NGS) enereferensi yofuzo

I-mRNA-seq (NGS) enereferensi yofuzo

I-RNA-seq iyithuluzi elivamile kuyo yonke impilo nesayensi yezitshalo, elivala igebe phakathi kwama-genome nama-proteome. Amandla ayo asekutholeni imibhalo emisha kanye nokulinganisa ukusho kwayo esivivinyweni esisodwa. Isetshenziswa kakhulu ekuqhathaniseni izifundo ze-transcriptomic, ekhanyisa izakhi zofuzo ezihlobene nezici ezihlukahlukene noma ama-phenotypes, njengokuqhathanisa okuguquguqukayo nezinhlobo zasendle noma ukuveza ukubonakaliswa kofuzo ngaphansi kwezimo ezithile. I-BMKCloud mRNA(Reference) APP ihlanganisa ubuningi benkulumo, ukuhlaziywa kwesisho esihlukanisayo(DEG), kanye nesakhiwo sokulandelana sihlaziya kuphayiphi le-mRNA-seq(NGS) ye-bioinformatics futhi ihlanganise amandla esofthiwe efanayo, iqinisekisa ukusebenziseka kalula nokusebenziseka kalula. Abasebenzisi bangalayisha idatha yabo ye-RNA-seq efwini, lapho Uhlelo Lokusebenza lunikeza isixazululo esiphelele sokuhlaziywa kwe-bioinformamatic, esitobhini esisodwa. Ukwengeza, ibeka kuqala ulwazi lwekhasimende, ihlinzeka ngemisebenzi yomuntu siqu ehambisana nezidingo ezithile zabasebenzisi. Abasebenzisi bangasetha amapharamitha futhi bahambise umgomo wepayipi ngokwabo, bahlole umbiko osebenzisanayo, babuke idatha/imidwebo futhi baqedele ukumbiwa kwedatha, njengalokhu: ukukhethwa kofuzo okuhlosiwe, ukuhlanganisa okusebenzayo, umdwebo, njll.

Imiphumela yedemo

Ukumbiwa kwedatha

Imfuneko yokungenisa

Ukuhlaziya okuyinhloko

Ireferensi

Imiphumela yedemo

Ukumbiwa kwedatha

Imfuneko yokungenisa

Inkundla:Ilumina, MGI
Isu:I-RNA-Seq
Isakhiwo: Idatha ebhanqiwe, ehlanzekile.
Uhlobo lwelabhulali:fr-unstranded, fr-firststrand noma fr-secondstrand
Ubude bokufunda:150 bp
Uhlobo lwefayela:*.fastq, *.fq, *.fastq.gz noma *.fq.gz. Uhlelo luzokwenzabhanqa ngokuzenzakalelayo amafayela we-.fastq ngokwamagama efayela lawo,isb *_1.fastq ibhangqwe *._2.fastq.
Inombolo yamasampuli:Ayikho imikhawulo enambeniyamasampula, kodwa isikhathi sokuhlaziya sizokhula njengenani leamasampula akhula.
Inani Ledatha Elinconyiwe:6G isampula ngayinye

Ukuhlaziya okuyinhloko

Ukuhlaziywa okuyinhloko kanye namathuluzi we-bioinformamatic we-mRNA-seq (Reference)iphayiphi imi kanje:

1. Ukulawulwa Kwekhwalithi Yedatha:

•Ukususwa kokulandelana kwekhwalithi ephansi, ukulandelana kwe-adaptha,njll;

•Amathuluzi: amapayipi akhiwe ngaphakathi endlini;

2. Ukuqondanisa idatha ku-genome eyireferensi:

•Ukuqondanisa ukufundwa ne-algorithm eqaphela i-splice ngokumelene ne-i-genome yereferensi.

•Amathuluzi:I-HISAT2, ama-samtools

3. Ukuhlaziywa kwekhwalithi yelabhulali:

•Faka ukuhlaziywa kobude, ukuhlaziya ukugcwaliswa kwesikhala kokulandelana, njll;

•Amathuluzi:ama-samtools;

4. Ukuhlaziywa kwesakhiwo sokulandelana:

•Ukuhlaziya okuhlukile kokuhlanganisa, ukuthuthukiswa kwesakhiwo sofuzo,ukubikezela kofuzo lwenoveli, njll;

•Amathuluzi:I-StringTie, gffqhathanisa, I-GATK,UDIYAMOND, I-InterProScan, futhiHMMER.

5. Ukuhlaziywa kwenkulumo okuhlukile:

•Ukuhlolwa kwe-DEG, ukuhlaziywa kobudlelwano, ukusebenza kahleukunothisa;

•Imiphumela ehlukahlukene yokubona;

•RngeSEGSEQ, DESeq2, ggplot2, I-DEXSeq

Ireferensi

1. Kim, Daehwan et al. "Ukulungiswa kwe-genome okusekelwe kugrafu kanyei-genotyping nge-HISAT2 kanye ne-HISAT-genotype.”ImveloI-Biotechnology37 (2019): 907 - 915.

2. McKenna, Aaron et al. “I-Genome Analysis Toolkit: aImephuYehlisa uhlaka lokuhlaziya i-DNA yesizukulwane esilandelayoukulandelana kwedatha.”Ucwaningo lwe-genome20 9 (2010): 1297-303.

3. Li, Heng et al. “Ifomethi yokulandelana kokuqondisa/imephu kanyeAma-SAMtools.”I-Bioinformatics25 (2009): 2078 - 2079.

4. Perțea, Mihaela et al. "I-StringTie yenza ngconoukwakhiwa kabusha kwe-transcriptome evela ku-RNA-seq ifundeka.ImveloI-Biotechnology33 (2015): 290-295.

5. Uthando, uMichael I. et al. “Isilinganiso esilinganiselwe sokushintsha kokugoqa kanyeukusatshalaliswa kwedatha ye-RNA-seq nge-DESeq2.”I-GenomeIbhayoloji15 (2014): n. ikhasi.

6. U-Eddy, uSean R.. “Usesho Lwephrofayela Esheshisiwe ye-HMM.”I-PLoS I-Computational Biology7 (2011): n. ikhasi.

I-mRNA-seq (NGS) enereferensi yofuzo

I-mRNA-seq (NGS) enereferensi yofuzo

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