Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How can i use bowtie to map solid data

    Dear Sir or Madam:
    i am a fresh man to solid data and bowtie.
    I try to aln my reads file to human genome wiith command:

    "/data1/tools/bowtie-0.12.7/bowtie -q -p 6 -l 27 -n 2 -m 3 -e 950 -k 1 -S /data5/project/luo/index/Human_Genome SRR121550.fastq SRR121550.sam"

    and get the following error message:
    #################
    Reads file contained a pattern with more than 1024 quality values.
    Please truncate reads and quality values and and re-run Bowtie
    ##################

    then i checked my fastq file and i found the fastq file contain the reads info like this

    :@SRR121551.5 r1ahead05_20090410_1_cd4_5_8_1_32_149 length=35
    T32222220222201131111312222111131212
    +SRR121551.5 r1ahead05_20090410_1_cd4_5_8_1_32_149 length=35
    !7;/&##%'&'#$''&$&/'-)-%#$#*&$1$%#%.

    it's seems not a valid fastq file , but why??


    I use the followling command to dump sra to fastq

    /data1/tools/sratoolkit.2.1.9-centos_linux64/fastq-dump /data6/nuclesome/SRR155510.sra

    pls help ! thx!!!

  • #2
    The bowtie command needs -C, as it is color space. Which is also why your reads are like this: T32222220222201131111312222111131212

    Not sure if there are any other problems with your fastq file but I would try adding -C to the bowtie command and see if it works.

    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
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X