Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie2

    Hello,

    I tried to work with bowtie2 under Linux, but I faced many problems:
    1- The command (bowtie2) is not working as it's written in the manual of Bowtie 2 package but normal commands as bowtie and bowtie build are working.
    2- the example which is with the package lambda_virus , the basename is not recognized although the index files have this basename, so no alignment is allowed, I tried to build other indexes for other genome and set new basename by bowtie builder, but again the new basename is not recognized by bowtie2
    I use the same commands with bowtie1 without any problems so far.

    Thanks,
    Layal

  • #2
    bowtie isn't a normal command with bowtie2. Are you keeping bowtie in your PATH along with bowtie2?

    If you build your ebwt in the /examples/reference directory
    Code:
    bowtie2-build lambda_virus.fa lambda_virus
    Then run the example in the reference directory
    Code:
    bowtie2 -x lambda_virus -U ../reads/reads_1.fq -S eg1.sam
    Output is:

    10000 reads; of these:
    10000 (100.00%) were unpaired; of these:
    596 (5.96%) aligned 0 times
    9404 (94.04%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
    94.04% overall alignment rate
    Did you use bowtie-build or bowtie2-build? Don't have a copy of bowtie anymore (switched over to bowtie2), so I can't say if bowtie and bowtie2 indexes are compatible. Pretty sure they aren't, but I can't test it in front of me.

    If you built with bowtie-build instead of bowtie2-build, it /might/ be the problem.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      Today, 06:43 AM
    • seqadmin
      Best Practices for Single-Cell Sequencing Analysis
      by seqadmin



      While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
      06-06-2024, 07:15 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 06-21-2024, 07:49 AM
    0 responses
    224 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-20-2024, 07:23 AM
    0 responses
    232 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-17-2024, 06:54 AM
    0 responses
    231 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-14-2024, 07:24 AM
    0 responses
    28 views
    0 likes
    Last Post seqadmin  
    Working...
    X