Dubcovsky Lab | Resources for Wheat Genetics & Breeding

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

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