mRNA-seq (NGS) ine referensi genome

mRNA-seq (NGS) ine referensi genome

RNA-seq chishandiso chakajairwa muhupenyu nesainzi yezvirimwa, kuvhara mukaha uripo pakati pe genomes nemaproteomes. Simba rayo riri mukuwana zvinyorwa zvitsva uye kuenzanisa kutaura kwavo mune imwe bvunzo. Inoshandiswa zvakanyanya pakuenzanisa zvidzidzo zvezvinyorwa, ichijekesa majini ane hukama neakasiyana hunhu kana phenotypes, sekuenzanisa mutants nemhando dzesango kana kuburitsa gene mataurirwo pasi pemamiriro chaiwo. BMKCloud mRNA (Reference) APP inosanganisa chiyero chekutaura, kusiyanisa kutaura kwekuongorora (DEG), uye kutevedzana dhizaini inoongorora muRNA-seq(NGS) bioinformatics pombi uye inosanganisa kusimba kwesoftware yakafanana, kuve nechokwadi chekureruka uye mushandisi-ushamwari. Vashandisi vanogona kurodha yavo RNA-seq data kune gore, uko App inopa yakazara, imwe-inomira bioinformatic yekuongorora mhinduro. Pamusoro pezvo, inokoshesa ruzivo rwevatengi, ichipa maitiro emunhu anoenderana nezvinodiwa nevashandisi. Vashandisi vanogona kuseta maparamendi uye kuendesa iyo pombi mishoni vari voga, tarisa iyo inopindirana mushumo, tarisa data / dhayagiramu uye yakazara migodhi yedata, senge: kusarudzwa kwemajini, kubatanidza kunoshanda, dhizaini, nezvimwe.

Demo results

Data mining

Import zvinodiwa

Kuongorora kukuru

Reference

Demo results

Data mining

Import zvinodiwa

Platform:Ilumina, MGI
Nzira:RNA-Seq
Layout: Paried, yakachena-data.
Mhando yeraibhurari:fr-unstranded, fr-firststrand kana fr-secondstrand
Kureba kwekuverenga:150 bp
Mhando yefaira:*.fastq, *.fq, *.fastq.gz kana *.fq.gz. Iyo system ichaitabatanidza otomatiki mafaira e.fastq maererano nemazita emafaira,eg *_1.fastq yakabatanidzwa ne *._2.fastq.
Nhamba yemasampuli:Hapana zvirambidzo pane nhambayemasampuli, asi nguva yekuongorora ichawedzera sehuwandu hwesamples inokura.
Yakakurudzirwa Data Mari:6G pamuenzaniso

Kuongorora kukuru

Iyo huru yekuongorora uye bioinformatic zvishandiso zvemRNA-seq (Reference)pipeline iri sezvinotevera:

1. Rawdata Quality Control:

•Kubviswa kwemhando yakaderera sequences, adapter sequences,etc;

• Zvishandiso: pombi yakagadzirwa mumba;

2. Kurongeka kwedata kune referensi genome:

•Kubatanidza kuverenga ne splice-aware algorithm inopesana nereference genome.

•Zvishandiso:HISAT2, samtools

3. Ongororo yemhando ye library:

•Isai kureba kuongorora, kutevedzana saturation kuongorora, etc;

•Zvishandiso:samtools;

4. Kutevedzana kwechimiro chekuongorora:

•Alternative splicing analysis, gene structure optimization,novel gene kufanotaura, etc;

•Zvishandiso:StringTie, gffcompare, GATK,DIAMOND, InterProScan,uyeHMMER.

5. Differential expression analysis:

• Kuongorora kweDEG, kuongororwa kwehukama, kushandaenrichment;

•Migumisiro yekuona yakasiyana;

•RpamweSEGseq, DESeq2, ggplot2, DEXSeq

Reference

1. Kim, Daehwan et al. "Graph-based genome alignment uyegenotyping neHISAT2 uye HISAT-genotype.NatureBiotechnology37 (2019): 907 - 915.

2. McKenna, Aaron et al. “The Genome Analysis Toolkit: aMepuDhedza chimiro chekuongorora chizvarwa chinotevera DNAkutevedza data."Genome research20 9 (2010): 1297-303 .

3. Li, Heng nevamwe. "The Sequence Alignment/Mepu fomati uyeSAMtools."Bioinformatics25 (2009): 2078 - 2079.

4. Perțea, Mihaela et al. "StringTie inogonesa kuvandudzwakuvakwazve kwechinyorwa kubva kuRNA-seq kuverenga. "NatureBiotechnology33 (2015): 290-295.

5. Rudo, Michael I. et al. "Kuyerwa kwakadzikama kwekupeta shanduko uyekuparadzirwa kweRNA-seq data neDESeq2. "GenomeBiology15 (2014): n. pag.

6. Eddy, Sean R.. "Yakakurumidza Kutsvaga Mbiri HMM."PLoS Computational Biology7 (2011): n. pag.

mRNA-seq (NGS) ine referensi genome

mRNA-seq (NGS) ine referensi genome

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