Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • newbie BWA alignment question

    another newbie question - I am trying to use BWA to align paired end reads to human ref genome.

    here is the sequence of what i did -
    1) alignment
    bwa align ref fq1 > 1.sai

    2) make sam
    bwi sampe ref 1.sai 2.sai fq1 fq2 > .sam

    3) convert to bam
    samtools view -S -b .sam -o .bam

    4) sort bam
    samtools sort .bam .sorted

    5) index bam
    samtools index .sorted

    6) check stats
    samtools flagstat .bam > .stat

    everything finished running without any error, but when i check the .stat file, this is what i see

    0 + 0 duplicates
    0 + 0 mapped (0.00%:nan%)
    61091524 + 0 paired in sequencing
    30545762 + 0 read1
    30545762 + 0 read2
    0 + 0 properly paired (0.00%:nan%)
    0 + 0 with itself and mate mapped
    0 + 0 singletons (0.00%:nan%)
    0 + 0 with mate mapped to a different chr
    0 + 0 with mate mapped to a different chr (mapQ>=5)

    in every sample, there is very few to no aligned reads. can anyone comment on what could possibly be the issue here and if there is a way to check the output after each stage in this process. thanks.

  • #2
    .sams are human readable. So start by looking at those.

    You did index the genome too, right?

    Comment


    • #3
      Did you align the second set of fastq sequences? All I see is
      bwa align ref fq1 > 1.sai
      but not
      bwa align ref fq2 > 2.sai

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Genetic Variation in Immunogenetics and Antibody Diversity
        by seqadmin



        The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
        11-06-2024, 07:24 PM
      • seqadmin
        Choosing Between NGS and qPCR
        by seqadmin



        Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
        10-18-2024, 07:11 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 11-08-2024, 11:09 AM
      0 responses
      59 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 11-08-2024, 06:13 AM
      0 responses
      38 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 11-01-2024, 06:09 AM
      0 responses
      35 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-30-2024, 05:31 AM
      0 responses
      23 views
      0 likes
      Last Post seqadmin  
      Working...
      X