Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bam and Sam don't like my fasta file

    Hello all,

    I have a sequence from the yeast s. cerevisiae containing at least 1 SNP. I formatted it into a fasta file using fastx formatter. Its fine if I use it with StandAloneBlast. I get an alignment, and its all fine. Then when I throw it into BAM/SAM, I don't seem to get anything. I tried it out on MAQ, and instead of doing the easyrun I broke it down step by step. When it was time to read in this file it could make the index file, but i got a message saying 0 sequences were loaded, and aborted on the next run. So I think I'm having the same problem with both SAM/BAM and MAQ.

    Code:
    jill@jill-desktop:~/maq/scripts$ maq fasta2bfa /home/jill/maq/Project/yeast.nt /home/jill/maq/Project/yeast.nt.bfa
    -- 17 sequences have been converted.
    jill@jill-desktop:~/maq/scripts$ maq fastq2bfq /home/jill/maq/Project/yeast.fasta  /home/jill/maq/Project/yeast.fasta.bfq
    -- finish writing file '/home/jill/maq/Project/yeast.fasta.bfq'
    -- 0 sequences were loaded.
    jill@jill-desktop:~/maq/scripts$ maq match /home/jill/maq/Project/yeast.map /home/jill/maq/Project/yeast.nt.bfa /home/jill/maq/Project/yeast.fasta.bfq
    -- maq-0.7.1
    [ma_load_reads] loading reads...
    [ma_load_reads] 0*2 reads loaded.
    [ma_longread2read] encoding reads... 0 sequences processed.
    maq: match.cc:569: int ma_match(int, char**): Assertion `size_l >= 12 && (size_r == 0 || size_r >= 12)' failed.
    Aborted
    yeast.fasta is my query, and yeast.nt is my reference.

    Here's the first bit of my yeast.fasta

    >Yeast
    NAGTTGTCATCCAGCTTCCATTACATCCGNNNNNNNNATGCAACTGGATGGAGAATGGCA
    AAATANNNNNNNNAGCATAAATTAAAATGAAGGAAATAACACNNNNNNNATACATTCCTA
    ATCATTTTTGTTTATTTCNNNNNNNGATCAACTTTTTATTTTTATTTTTATTTTNNNNNN
    NGTGTAATGCGGCAAAATGTTAGTGCAGGANNNNNNNTGTTCTTCAAAAAGGCGGAGTGG
    CTATGGAANNNNNGAGAATCTATGTTGGTTTATGTTCCGGAAGCNNNNNATCCATCCTTG
    TACGATCTGTATGTTTACTCNNNNNATTGCTTTACCTTTTGCATTTTCTTACTGGGNNNN
    NACGAAATAAACGCCACATAACAGTATAATGTNNNNNGTCCTGTTCAGACAAATTTTGAG
    CGATGCCGNNNNNGCCTATCATTACTGGCCCAATCGGCTTGTTTNNNNNAGGTTATCATC
    ACGTATATTGGAGATAATATNNNNNATGTCACTATTATCAACCTATCGATATCGAANNNN
    NCAACAATCAGCAAAACTACCAGCAATACAGCCNNNNAGACAATAATTGAACAAATCTTA
    TCCTTCTTACCTNATACAATACTGAGCATGAAGTTGCATAGCTTAAGCNATTTCAAGGTT
    TTGAATCCGTCGATAGTCTCATCANGTTC

    Any hints for me? I've been scratching my head over what the problem could be, and I got nothing.

    Thanks so much!

  • #2
    Are you trying to use fastq2bfq on a fasta file?

    Comment


    • #3
      Have you tried removing the whitespaces in the sequence? This is, by definition, not a sequence base ..

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X