Header Leaderboard Ad

Collapse

454 Reads correction with Short reads ?

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 454 Reads correction with Short reads ?

    Hello everybody,

    I can see that my 1Mio 454 reads are full of insertions/deletions in homopolymer regions, and of course this disrupts my ORFs in later stages (annotation step). Fortunately, I have ca 60mio Illumina reads that I can use to correct these errors. Both dataset are cDNA.

    Has anyone a preferred method to correct short sequencing error indels? If tractable, I would prefer correcting my reads rather than correcting my draft assembly obtained from those reads. I was going to use ssaha (or segemehl, qpalma, other?) to map the illumina reads on my 454 reads, and then extract a consensus by parsing the pileup file generated with samtools

    I have seen a few published, more advanced, methods available but I*do not now if one of them performs better (e.g. iCorn). Do you?

    Thanks a lot!

    Yvan

  • #2
    I don't know if any programs will correct your reads!

    See here for another effort .. I have got it to work but am still interpreting results

    http://seqanswers.com/forums/showthread.php?t=3635

    Comment


    • #3
      I did this once. My approach was to map the reads to the contigs (BWA -e5), realigned the indels using GATK and polished the contigs based on the the indel report. I did this multiple times as some corrections made it possible to correct other neighbouring regions.

      I dont have the polishing script any more, but I recall it as fairly simple. It should be possible to polish the reads instead, with some perl regex magic.

      Comment


      • #4
        Have you seen this paper?

        http://bioinformatics.oxfordjournals.../1284.abstract

        Comment

        Latest Articles

        Collapse

        • seqadmin
          A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
          by seqadmin


          ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

          01-24-2023, 01:19 PM
        • seqadmin
          Introduction to Single-Cell Sequencing
          by seqadmin
          Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

          The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
          ...
          01-09-2023, 03:10 PM

        ad_right_rmr

        Collapse
        Working...
        X