About

The hits is an integrated pipeline for DNA resequencing and RNAseq analyses in Xu Lab. It is designed for molecular biologists with limited bioinformatics skills. Experts can use it but please note that some of the parameters are built-in, you are your are warned here.

HIgh-Throughput Sequencing (hits) pipeline

hits 0.12.0

Usage:

    hits <option>

    -p  pipeline for DNAseq [D] or RNAseq [R] analysis
    -d  directory that containing FASTQ file(s), .fq/.fastq(.gz)
    -g  reference genome file
    -c  consensus genome file
    -l  leviosam lift index file
    -n  set ploidy [default 1, work with -p D]
    -a  annotation file in GTF format [work with -p R]
    -s  strand-specific information [work with -p R]
        1 - stranded [default]
        0 - unstranded
    -i  max intron length [work with -p R, default 4000 bp]
    -o  output directory
    -t  number of alignment threads
    -h  help
    -v  version

Examples:

    hits -p D -d fastq_dir -g genome.fa -o output_dir -t 8
    hits -p R -d fastq_dir -g genome.fa -a gene.gtf -s 1 -o output_dir -t 8

Reporting Bugs:

    Bug reports can be submitted via the web:
    https://github.com/xulab-nwafu/hits/issues

DNA resequencing pipeline

• For mapping and variants calling in DNA resequencing, use dnaseq

Usage: dnaseq fastq_directory
 e.g.: dnaseq ~/data/example/dnaseq/fastq

• To compare the differences between reference genome and variant genome(s) in VCF format, use vcfcmp in https://github.com/xulab-nwafu/filter_vcf

Usage: vcfcmp ref.vcf var1.vcf var2.vcf ...
 e.g.: vcfcmp WT.vcf MU.vcf

RNAseq pipeline

• For mapping and counting reads of each gene in RNAseq, use rnaseq

Usage: rnaseq fastq_directory
 e.g.: rnaseq ~/data/example/rnaseq/fastq

• To compare the differences between two RNA samples, use rnadiff in https://github.com/xulab-nwafu/rnadiff

Usage: rnadiff rnaseq.conf rnaseq.tsv control_tag case_tag
 e.g.: rnadiff demo/rnaseq.conf demo/rnaseq.tsv wt mu

• To perform Gene Ontology enrichment analysis, use goea in https://github.com/xulab-nwafu/seqmate/tree/master/misc

Usage: goea gene_id.txt
 e.g.: goea de.up.txt

Note

Please note that dnaseq, vcfcmp, rnaseq, and goea can only use for Fusuarium graminearum directly. Other species need to change a few of source codes. rnadiff could be applied to any species, if you like.

Dependence

• bowtie2
• hisat2
• samtools
• bcftools
• subread
• snpEff
• ontologizer
• graphviz
• R
• filter_vcf
• rnadiff
• leviosam

Author

Qinhu Wang ([email protected])

Copyright

2016-2022 (c) Xu Lab, Northwest A&F University

License

MIT