HemTools
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NGS pipelines
Data Visualization
Motif Analysis Suite
Integrative Analysis
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Installation
A collection of Jupyter Notebooks
Bioinformatic Tools
Predicting in vivo TFBS using Catchitt
Calling significant interactions from Capture-C or Capture-HiC
GSEA and pathway/GO enrichment analyses
Replicate correlation and QC for HiC data
Gene expression clustering
Consensus peaks given multiple (>=2) replicates
NCBI data submission
Local UCSC cell browser usage for Seurat
notes on alphafold
Assigning features to a bed file.
General bait design
calculate chrM percent
Filter bam files and generate bw files
check sample barcode frequency in index reads
Barcode frequency in 5’-end
Download raw data from Illumina Base Space
Convert BCL basecall files to FASTQ files
BedGraph to BigWiggle
bed overlap bedpe
Query bed overlap with a list of bed files
Merging bigwiggle files into one bw
Input
Usage
Chromatin interaction calling in captureC data
ATAC-seq model and footprint prediction using Chrombpnet
Summary
Input
Important note
Usage
Output
QC
Visualize genomic loci (overview)
Count indel integration pipeline
Count indel integration pipeline (simplified version)
Crispresso2 for HDR
Convert CRISPResso allele frequency table to vcf-like table
Interactive visualization using Dash Bio
convert dataframe to html
CRISPR Screening Demultiplexing
CRISPR Screening Demultiplexing (hard trim first N random bp)
Demultiplexing fastq files
Diff or merge of two bw files
DNAnexus download and upload
EGACryptor for EGA submission
Call interactions from HiC
Extract inward/outward oriented pairs from BAM file
Merge fastq I1 I2 R1 R2 reads into R1 and R2
subsample fastq and visualize in sequence logo
Run fastQC for a list of fastq files
Filter out reads mapped to specific sequences
Annotate vcf file (custom annotation not work)
Genomic features annotatoin given bed file
Extract user-defined gene promoter from refseq TSS database
Find allele (e.g., SNPs) specific effects
Integrating gene expression data and PPI network
Objective
Steps
Cons
Input
Usage
Output
GTF operations
Running GUIDE-seq in HPC
HiC-Pro
Generate indexed genome, chrom size, and res fragment bed for HicPro analysis
Homer ChIP-seq analysis
How to download all files from a website
ENCODE database query
Transcript-level abundance quantification
Kmer count over bed
Lift Over Bed or bigWiggle files
LiftOverVCF
Seurat to Loupe browser
Merge multiple bedfiles
Merge fastq files for L001 L002 L003 L004
Write flowchart using text
Using nf-core pipelines on HPC
OnTAD
Optimal subset finding problem in mutagenesis studies
Filtering out peaks in narrowPeak files
Convert rmd to html
RNA-seq QC
Across cell type NGS data normalization
single cell RNA-seq data integration
FASTQ files operations
Smoothing a bedgraph file
Download fastq data from NCBI SRA
Subsample fastq to the same sequencing depth
Super-enhancer identification
Convert a column to bigwiggle file
Using GPU on HPC
Test differences in number of interactions
Identify direct targets and co-binding factors
Extract Ensembl Gene Name and IDs given IDs or names from any databases
(TOBIAS) Footprint analysis for ATAC-seq data
Uditas
Generate new genome given vcf file
Accessible Data in HemTools
Gallery (stand-alone tools)
Differential Analysis pipelines
Study notes
Machine Learning pipelines
CRISPR tools
Bioinformatics Core Competencies
HemTools
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Bioinformatic Tools
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FASTQ files operations
FASTQ files operations
¶
1. convert fastq to fasta
seqtk
seq
-a
in
.fastq.gz
>
out.fasta
code @ github
.
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