HemTools
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NGS pipelines
Standard GATK variant calling for both human and non-human species
MNase-seq analysis pipeline (not a standard version)
MicroC data analysis pipeline
MinION Nanopore for sequence assembly and read mapping
Create normalized RNA-seq bigwiggle files
RNA velocity analysis
Analysis of single cell Strand-seq data
Analysis of Sci-L3-seq data
Targeted methyl-seq amplicon analysis
RNA-seq alternative splicing pipeline
ATAC-seq
Footprint analysis for ATAC-seq data
STARR-seq analysis pipeline
Running just BWA mem mapping
CaptureC data analysis pipeline
CHANGE-seq analysis pipeline
Paired-end ChIP-seq
Single-end ChIP-seq
CITE-seq (scRNA-seq with antibodies) analysis
Genome-wide CRISPR Screening
CUT & RUN pipeline
CUT & RUN calibration pipeline
Cut & RUN footprinting
nfcore pipelines for CUT-RUN, CUT-Tag, and TIPseq
Differential exon analysis
RNA-seq: differential gene expression analysis
eCLIP-seq data analysis pipeline
gCrisprTools: Genome-wide CRISPR Screening
RNA-seq: Identification of gene fusion events
Detecting allele-specific effects on ChIP-seq or ATAC-seq
Analysis of Hi-C or HiChIP data
MNase-based HiCHIP data analysis
Analysis of Hi-C and capture-C data using HiC-Pro
Paired-end histone ChIP-seq or CUT&RUN
Call IDR peaks given bam files from two replicates
PacBio iso-seq data analysis
DNA methylation (Bisulfite-Sequencing) analysis pipeline using nf-core
Call motif footprint from bigwiggle files
Inspection of multi-mapped reads
Sequencing-depth and fragment-length normalized bigwiggle track
Sequencing-depth and fragment-length normalized bigwiggle track
Total reads in peaks normalized bigwiggle track
Variant calling on PacBio HIFI reads
Summerize R1 R2 read mapping direction and distance
RNA-seq: Transcript-level quantification
Variant identification on RNA-seq data
scJupyter for single cell integration, annotaiton, modeling and reporting
SHARE-seq data analysis
Single-cell RNA-seq analysis
Single-cell RNA-seq analysis
Single-cell multiomc analysis
SLAM-seq for time-resolved RNA sequencing
NCBI download GEO/SRA data
STARR-seq analysis pipeline
Target-Seq analysis
HemTools Tutorial 4-18-2019
Typical Usage
Sample input format
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Running just BWA mem mapping
Running just BWA mem mapping
ΒΆ
run_lsf
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py
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f
fastq
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tsv
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p
bwa_mem
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g
mm9
code @ github
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