Open in new window

• Before starting: enable SIMD in your web browser (see Help below).
• This tool is for paired-end fastq files (i.e., xxx_R1_001.fastq.gz and xxx_R2_001.fastq.gz). It uses HISAT2 to find big deletions (treated as introns).
• Please run the three steps below to obtain the indexed BAMs from a list of FASTQ files.
• In the end, you will receive a summary file of indels and all the BAM files to be viewed in IGV.
• No spaces are allowed in input file names.
  
  Junli Zhang 2022-05-01

• See Help below on your first use
  
  Junli Zhang 2020-11-15 

• Please paste gene IDs (e.g. TraesCS5A02G391700) or specific cDNA IDs (e.g. TraesCS5A02G391700.2) below.
• Each line is a gene.

• Find potential wheat homeologs (best hit with >90% identity and alignment >60% of the CDS length) and their functions based on Arabidopsis (At) and rice (Os) blast results (top 1 hit).
• Please paste gene IDs (e.g. TraesCS5A02G391700) below. Each line is a gene.
• To start a new job, click the “Clear” button below and resubmit (faster than refreshing the page).
  
  Junli Zhang 2024-07-23 

• Match the genes in CS RefSeq v1.1 annotation HC with Kronos v1.0 annotation (best hit with >97% identity and alignment length > 100 bp).
• Some genes may have multiple hits or not on the same chromosome. Select with your own eyes based on chromosome matches and %identity.
• Please paste gene IDs (e.g., TraesCS5A02G391700) or transcript IDs (e.g., TraesCS5A02G391700.1; the tool will convert them to gene IDs). Each line is a gene.
• The output will be the best-matching transcript IDs.
  
  Junli Zhang 2024-07-26 

Extract cDNA sequences from CS and Kronos
Find wheat potential homeologs
Gene ID conversion between Kronos and CS

CRISPR Editing Analysis
CRISPR NGS editing check with HISAT2

Acknowledgments to Junli Zhang (https://junli.netlify.app/)