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.
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
- 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
vcfcmpin https://github.com/xulab-nwafu/filter_vcf
Usage: vcfcmp ref.vcf var1.vcf var2.vcf ...
e.g.: vcfcmp WT.vcf MU.vcf
- 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
rnadiffin 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
goeain https://github.com/xulab-nwafu/seqmate/tree/master/misc
Usage: goea gene_id.txt
e.g.: goea de.up.txt
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.
- bowtie2
- hisat2
- samtools
- bcftools
- subread
- snpEff
- ontologizer
- graphviz
- R
- filter_vcf
- rnadiff
- leviosam
Qinhu Wang ([email protected])
2016-2022 (c) Xu Lab, Northwest A&F University
MIT