FANSe protocols

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FANSe specifications

Information


Unique identifier OMICS_04840
Name FANSe
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability No
Maintained No

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Publication for FANSe

FANSe in pipelines

 (2)
2016
PMCID: 4964843
PMID: 27516766
DOI: 10.3389/fpls.2016.01125

[…] generated 2 × 100 bp paired-end reads., the clean sequencing reads were mapped to the rice rna reference sequence (msu release7, downloaded from http://rice.plantbiology.msu.edu/index.shtml) using fanse 2 algorithm (zhang et al., ) with the parameters −l110 −e7 −u0 −s10. the transcripts with at least five mapped reads out of eight samples were considered as reliably detected transcripts. […]

2015
PMCID: 4350611
PMID: 25644173
DOI: 10.1186/s12943-014-0285-x

[…] fluorescence-activated cell sorting (facs) analysis., the sequencing reads were mapped to the mouse refseq-rna reference sequence (downloaded from http://hgdownload.cse.ucsc.edu/downloads) using the fanse 2 algorithm (http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters − l85 − e3 − u0 − s10 []. reads mapped with tophat2 were associated with genes using the custom perl scripts […]


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FANSe in publications

 (9)
PMCID: 5722806
PMID: 29255466
DOI: 10.3389/fimmu.2017.01713

[…] analysis usually indicated purities of >95%., the sequencing reads were mapped to the mouse refseq-rna reference sequence (downloaded from http://hgdownload.cse.ucsc.edu/downloads) using the fanse 2 algorithm (available from http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters −l85 −e3 −u0 −s1015. alternative splice variants were merged. genes with at least 10 mapped […]

PMCID: 5429708
PMID: 28396609
DOI: 10.1038/s41598-017-00914-1

[…] number of reads per kilobase of exon model per million mapped reads (fpkm) to obtain normalized gene expression levels. we mapped the original rna-seq to the reference transcriptome sequence using fanse2 as previously described. the correlation coefficients between gene expression levels were calculated and plotted as a correlation heatmap. gene ontology (go) analysis was performed using topgo […]

PMCID: 5293807
PMID: 28223918
DOI: 10.3389/fnmol.2017.00027

[…] 2 n (ambiguous nucleotides) were retained. moreover, paired reads that mapped to the silva database were discarded. the cleaned reads of each sample were aligned to the mouse rna ensembl database by fanse2, allowing 7 nucleotide mismatches. all unigene clusters with at least 10 mapped reads were considered as reliable transcripts. to analyze differentially expressed unigenes, the expression […]

PMCID: 5137168
PMID: 27917918
DOI: 10.1038/srep38411

[…] reproducible genes expression profiles ()., clean sequencing reads were mapped to the human ensembl-rna reference sequence (downloaded from http://asia.ensembl.org/homo_sapiens/info/index) using the fanse 2 algorithm with the parameters -l110 -e7 -u0 -s10. alternative splice variants were merged. genes with at least 10 mapped reads were considered to be reliably detected genes. these genes […]

PMCID: 4964843
PMID: 27516766
DOI: 10.3389/fpls.2016.01125

[…] generated 2 × 100 bp paired-end reads., the clean sequencing reads were mapped to the rice rna reference sequence (msu release7, downloaded from http://rice.plantbiology.msu.edu/index.shtml) using fanse 2 algorithm (zhang et al., ) with the parameters −l110 −e7 −u0 −s10. the transcripts with at least five mapped reads out of eight samples were considered as reliably detected transcripts. […]


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FANSe institution(s)
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
FANSe funding source(s)
Supported by the National ‘‘973’’ Projects of China (2011CB910700), National Natural Science Foundation of China (31300649 and 31200612), the Key Project of Chinese Ministry of Education (212207), Guangdong Natural Science Foundation (S2013010013529), Foundation for Distinguished Young Talents in Higher Education of Guangdong, China (2012LYM_0026), the Fundamental Research Funds for the Central Universities (21612202, 21612459, 11610101, 21613343 and 21611201), and the Institutional Grant of Excellence of Jinan University, China (50625072).

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