Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • index reference file to use for bowtie

    I am trying to run Bowtie on a small test fastq file. It is human hg19 build. I found that the index file can be downloaded from the right panel of this:



    The downloaded files are:

    hg19.1.bt2
    hg19.2.bt2
    hg19.3.bt2
    hg19.4.bt2
    hg19.rev.1.bt2
    hg19.rev.2.bt2
    hg19.zip
    make_hg19.sh

    make_hg19.sh requires bowtie2. and I don't have authorization to install bowtie2 onto our server.

    Since hg19 must be a very common reference, is there anyplace that we can directly download the indexed file of hg19? what is the appendix for this index file?

    thanks

  • #2
    Bowtie(1) needs a Bowtie(1) library, it can't use a Bowtie2 library. Assuming you already have Bowtie installed then make the library using the 'bowtie-build' command. You should upgrade to bowtie2 though, it is much better.

    Comment


    • #3
      Thanks I see

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • 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...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 07-10-2024, 07:30 AM
      0 responses
      25 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-03-2024, 09:45 AM
      0 responses
      201 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-03-2024, 08:54 AM
      0 responses
      211 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-02-2024, 03:00 PM
      0 responses
      193 views
      0 likes
      Last Post seqadmin  
      Working...
      X