Header Leaderboard Ad

Collapse

BWA-MAQ questions?

Collapse

Announcement

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

  • BWA-MAQ questions?

    We have RNA-Seq paired-end data, the insert size is about 200bp , and the read length is different.

    4_1.fq 50bp
    4_2.fq 36bp

    5_1.fq 75bp
    5_2.fq 50bp

    Can i run

    bwa aln database.fasta 4_1.fq 4_2.fq 5_1.fq 5_2.fq > aln_sa.sai


    How BWA do paired-end alignment for different read length?

    And there are many situations like : one read is in one exon ,the other read is in other exon, the mapping position of these two reads on genome is 500, 3600. The distance is 3100 (there is a intron there) and BWA will discard these paired-end reads alignment because their distance is signicicant larger than 200bp?

    Or i should map these reads as single reads?
    Last edited by baohua100; 08-04-2009, 08:44 PM. Reason: Questions about aligning paired-end RNA-seq reads using BWA‏

  • #2
    Firstly, you will have to align fastq file individually to get correspond suffix array files, as

    bwa aln database.fasta 4_1.fq > 4_1.fq.sai
    bwa aln database.fasta 4_2.fq > 4_2.fq.sai
    bwa aln database.fasta 5_1.fq > 5_1.fq.sai
    bwa aln database.fasta 5_2.fq > 5_2.fq.sai

    Then use sampe to generate results in sam format, I never align PE reads with different length, but I guess you may be able to get result sam files, just displaying different length at SEQ and QUAL fields. (Try and let us know what you get)

    I have no idea about the insert size issue, as bwa is a new tool, everyone is doing experiements on that.

    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
    • 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

    ad_right_rmr

    Collapse
    Working...
    X