Fastq_clean: An optimized pipeline to clean the Illumina sequencing data with quality control

Zhang, Mi; Sun, Honghe; Fei, Zhangjun; Zhan, Feng; Gong, Xiujun; Gao, Shan

doi:10.1109/bibm.2014.6999309

Cited by 73 publications

(51 citation statements)

References 23 publications

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“…13 Fastq_clean is a Perl based pipeline to clean DNA-seq, 14 RNA-seq 15 and sRNA-seq data 16 with quality control and had included some tools to process Pacbio data in the version 2.0. The software BWA v0.7.12 was used to align draft transcripts to the complete E. fullo mitochondrial genome.…”

Section: Discussionmentioning

confidence: 99%

PacBio full-length transcriptome profiling of insect mitochondrial gene expression

et al. 2016

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In this study, we sequenced the first full-length insect transcriptome using the Erthesina fullo Thunberg based on the PacBio platform. We constructed the first quantitative transcription map of animal mitochondrial genomes and built a straightforward and concise methodology to investigate mitochondrial gene transcription, RNA processing, mRNA maturation and several other related topics. Most of the results were consistent with the previous studies, while to the best of our knowledge some findings were reported for the first time in this study. The new findings included the high levels of mitochondrial gene expression, the 3 0 polyadenylation and possible 5 0 m 7 G caps of rRNAs, the isoform diversity of 12S rRNA, the polycistronic transcripts and natural antisense transcripts of mitochondrial genes et al. These findings could challenge and enrich fundamental concepts of mitochondrial gene transcription and RNA processing, particularly of the rRNA primary (sequence) structure. The methodology constructed in this study can also be used to study gene expression or RNA processing of nuclear genomes.

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Section: Discussionmentioning

confidence: 99%

PacBio full-length transcriptome profiling of insect mitochondrial gene expression

et al. 2016

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“…RNA‐seq libraries were constructed as previously described and sequenced on a HiSeq 2500 system according to the manufacturer's instructions with sequencing at 125 bp (PE125, library size is 280–320 bp). The software Fastq_clean was used for RNA‐seq data cleaning and quality control (Zhang et al ., ). The raw RNA‐seq reads were filtered with Fastq_clean software by trimming low‐quality (Q value < 20) nucleotides on both ends, clipping the adapter and barcode sequences from the 3′ end, and discarding the ribosomal RNA (rRNA) sequence.…”

Section: Methodsmentioning

confidence: 99%

Genome‐wide analysis of odorant‐binding proteins and chemosensory proteins in the sweet potato whitefly, Bemisia tabaci

Zeng

Yang

et al. 2018

Insect Science

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Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) of insects are thought to play roles in olfactory recognition affecting host choice, copulation, reproduction and other behaviors. Previous descriptions of OBPs and CSPs in the whitefly Bemisia tabaci often provided no or incomplete genetic information. In this study, we present a genome-wide and transcriptome-wide investigation of the OBPs and CSPs in B. tabaci MEAM1 (Middle East-Asia Minor1 species). Eight OBP and 19 CSP genes were identified that covered all previous sequences. Phylogenetic analyses showed that the CSP genes had a lineage-specific expansion (BtabBCSP1, BtabBCSP3, BtabBCSP13, BtabBCSP17, BtabBCSP18 and BtabBCSP19). Expression profiling of OBPs and CSPs by transcriptome sequencing and quantitative real-time polymerase chain reaction (qPCR) revealed that expression patterns differed among developmental stages of B. tabaci MEAM1. Five OBP genes and 11 CSP genes significantly differed between males and females; four of the 19 CSP genes were highly expressed in adults, while two were highly expressed in nymphs. The expression profiles of the OBP and CSP genes in different tissues of B. tabaci MEAM1 adults were analyzed by qPCR. Four OBP genes found in B. tabaci MEAM1 were highly expressed in the head. Conversely, only two CSPs were enriched in the head, while the other six CSPs were specifically expressed in other tissues. Our results provide a foundation for future research on OBPs and CSPs in B. tabaci.

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“…Low-quality (with < 20 Phred scores) reads in raw reads were removed with Fastq_clean (Zhang M. et al, 2014) and assessed with FASTQC 1 . Clean reads were assembled using Trinity (version 2.0.6) with default parameters (Grabherr et al, 2011; Haas et al, 2013).…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptome Analysis between Gynoecious and Monoecious Plants Identifies Regulatory Networks Controlling Sex Determination in Jatropha curcas

Chen

Pan

et al. 2017

Front. Plant Sci.

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Most germplasms of the biofuel plant Jatropha curcas are monoecious. A gynoecious genotype of J. curcas was found, whose male flowers are aborted at early stage of inflorescence development. To investigate the regulatory mechanism of transition from monoecious to gynoecious plants, a comparative transcriptome analysis between gynoecious and monoecious inflorescences were performed. A total of 3,749 genes differentially expressed in two developmental stages of inflorescences were identified. Among them, 32 genes were involved in floral development, and 70 in phytohormone biosynthesis and signaling pathways. Six genes homologous to KNOTTED1-LIKE HOMEOBOX GENE 6 (KNAT6), MYC2, SHI-RELATED SEQUENCE 5 (SRS5), SHORT VEGETATIVE PHASE (SVP), TERMINAL FLOWER 1 (TFL1), and TASSELSEED2 (TS2), which control floral development, were considered as candidate regulators that may be involved in sex differentiation in J. curcas. Abscisic acid, auxin, gibberellin, and jasmonate biosynthesis were lower, whereas cytokinin biosynthesis was higher in gynoecious than that in monoecious inflorescences. Moreover, the exogenous application of gibberellic acid (GA3) promoted perianth development in male flowers and partly prevented pistil development in female flowers to generate neutral flowers in gynoecious inflorescences. The arrest of stamen primordium at early development stage probably causes the abortion of male flowers to generate gynoecious individuals. These results suggest that some floral development genes and phytohormone signaling pathways orchestrate the process of sex determination in J. curcas. Our study provides a basic framework for the regulation networks of sex determination in J. curcas and will be helpful for elucidating the evolution of the plant reproductive system.

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Fastq_clean: An optimized pipeline to clean the Illumina sequencing data with quality control

Cited by 73 publications

References 23 publications

PacBio full-length transcriptome profiling of insect mitochondrial gene expression

PacBio full-length transcriptome profiling of insect mitochondrial gene expression

Genome‐wide analysis of odorant‐binding proteins and chemosensory proteins in the sweet potato whitefly, Bemisia tabaci

Comparative Transcriptome Analysis between Gynoecious and Monoecious Plants Identifies Regulatory Networks Controlling Sex Determination in Jatropha curcas

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