Tools

  • Gene ID conversion between Kronos and CS
  • Find wheat potential homeologs
  • Extract cDNA sequences
  • Short read de novo assembly with Velevet
  • CRISPR editing check with BWA and SAMTOOLS v2
  • CRISPR NGS editing check with HISAT2
  • Make bam files with strobeAlign
  • Shade sequence alignments with nimBoxshade
  • Shade sequence alignments with Boxshade
  • Design KASP primers with Primer3 v2.5.0
  • Convert a vcf file to SNP table
  • Call variants with exactSNP
  • Index bams with SAMTOOLS
  • Format FASTA to fixed length
  • Make bams and indel calls with Subread
  • Filter fastq files with FASTP
  • Filter multiple fastq files with FASTP
  • Make bam files with BWA and SAMTOOLS
  • CRISPR Editing Analysis v2
  • Demultiplex a Fastq File
  • CRISPR Editing Analysis
  • Call SNPs from multiple sequence alignment
  • Reverse complement of DNA sequences

    • Gene ID conversion between Kronos and CS

    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).

    I did not do more filtering than that, so 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 (TraesCS5A02G391700.1, will be converted to gene IDs by the tool) below. Each line is a gene.

    Output will be the best matching transcript IDs.

    Gene ID conversion:


    Output below

    or Export to CSV

    Kronos transcript ID CS transcript ID %identity alignment length Kronos CDS length CS CDS length