Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    I have generated fastq files (R1& R2) from the mapped bam file and I am now interested in assembling those reads using velvet. I need guidance to how to run velveth, velvetg and viewing the output.

    Comment


    • #17
      Originally posted by Michael.Ante View Post
      Hi Kaps,

      you should have a look at the Bowtie2 homepage. There, it is explained in detail how the programs work. At the end of the manual is a "Lambda phage example", which has quite an overlap to your problem. It also has a SAMtools downstream section...

      Cheers,
      Michael
      I have used a reference (comprising of 2 sequences varying in length) to do alignment on paired end fastq files. I have generated the sam file but when i try converting it (sam) to bam, it is not working!
      here is the feedback: samtools view -bS 4_S4_paired.sam 4_S4_paired.bam
      [main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
      ▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
      ▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒֋▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
      ▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
      ▒▒y▒▒

      when with -bT, I get a similar feedback as;
      samtools view -bT cp4genome.fa 4_S4_paired.sam 4_S4_paired.bam
      [samfaipath] build FASTA index...
      [fai_build_core] different line length in sequence '4_S4_contig_23'.
      [samfaipath] fail to build FASTA index.
      [main_samview] random alignment retrieval only works for indexed BAM or CRAM files.
      ▒BC▒m▒▒N▒0D▒ܜK▒X=p[▒qU|
      ▒ ▒▒▒5r[SY▒I▒▒▒O▒sH[@▒▒▒f▒▒▒a0▒w3▒Rʄq▒▒G▒[▒2▒▒Q▒Lk▒֋▒ vU▒1)J▒ei▒M&"▒qq5▒Q^ݒ▒▒▒▒▒`▒ U▒▒▒Q▒ vI▒▒▒f▒▒q▒▒:;▒=▒▒P▒▒U▒▒"n\o3▒ε▒
      ▒;*(n▒J)*▒▒▒▒֙%▒zM19H▒I▒▒▒▒▒5{▒>▒S▒H▒Qt▒~▒▒▒
      where is the problem?

      Comment


      • #18
        Hi Kaps,

        try
        Code:
        samtools view -S 4_S4_paired.sam | head
        if you don't get any problems there, proceed with
        Code:
         samtools view -bSh 4_S4_paired.sam > 4_S4_paired.bam
        The missing '>' was then the problem. If the sam file doesn't have any header lines, you'll need to provide these additionally.

        Cheers,

        Michael

        Comment


        • #19
          its working.

          Thanks

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM
          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            02-26-2024, 02:07 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-14-2024, 06:13 AM
          0 responses
          34 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-08-2024, 08:03 AM
          0 responses
          72 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-07-2024, 08:13 AM
          0 responses
          81 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-06-2024, 09:51 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X