Header Leaderboard Ad


75mer mapping with BOWTIE



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

  • 75mer mapping with BOWTIE

    Hey all,

    I'm looking for some input on tuning BOWTIE for 75mer RNA-seq reads from mus - any suggestions? I'm currently allowing only unique hits, and using 68bp as seed length, but that may be too conservative.

    Johannes Waage
    Uni. of Copenhagen

  • #2
    Hi Johannes,

    That's certainly reasonable; I suggest doing a series of runs using your target data but also using the -u parameter to cut the job off after a certain number of reads so that it doesn't take forever. Doing several such runs with different sets of parameters (but the same -u) should help you determine the sweet spot w/r/t speed and sensitivity.



    • #3

      We are doing this routinely. We typically use the -v 2 option and use an index made from both the genome and splice junctions with 69 nt on either side of the junction. Surprisingly, we get a very large fraction of reads that map uniquely using these parameters.



      • #4
        Hi Johannes:
        How do you deal with exon junctions? some exons will be shorter than 75bps. Try tophat?



        • #5
          Can you tell me what reference are you using?


          • #6
            Originally posted by drio View Post
            Can you tell me what reference are you using?
            mm9 combined with a combinatorial exon-exon DB (142mers, requiring overlap of 4nt)


            Latest Articles


            • 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
            • seqadmin
              AVITI from Element Biosciences: Latest Sequencing Technologies—Part 6
              by seqadmin
              Element Biosciences made its sequencing market debut this year when it released AVITI, its first sequencer. The AVITI System uses avidity sequencing, a novel sequencing chemistry that delivers higher quality data, decreases cycle times, and requires lower reagent concentrations. This new instrument reportedly features lower operating and start-up costs while maintaining quality sequencing.

              Read type and length
              AVITI is a short-read benchtop sequencer that also offers an innovative...
              12-29-2022, 10:44 AM