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  • #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.

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    • #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

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