Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to remove 3'-adaptor sequence from illumina DGE expression data

    I got the raw illumina DGE expression data in FASTQ format, and trying to remove the 3'-adaptor sequence from it.

    here is samples of the raw data I got from the sequencing company
    @FC81M3VABXX:4:1101:1130:2169#0/1
    GGATCTGGTTGGGTTATCCAGTACTTCTCGTATGGCGTCTTCTGCTTGA
    +
    eceaeedec_bddI_c^bccebUecRc^cXXZ__L^BBBBBBBBBBBBB
    @FC81M3VABXX:4:1101:1110:2188#0/1
    TTCAGGTGGTTTCTTCTCCAGTACTTCTCGTATGCCGTCTTCTGCTTGA
    +
    gggggfdffdgggggggggdgggggggggedfeefffdfefd^aeefa^
    @FC81M3VABXX:4:1101:1184:2239#0/1
    GAACATCACTGTAGACTTCCAGTACTTCTCGTATGCCGTCTTCTGCTTG
    +
    fffffffffffefMfdddddffeffffeffe[db[eedbceecececd^

    I can find the Gex Adapter 2 for NlaIII gene expression (TCGTATGCCGTCTTCTGCTTG) at the end of the sequence, but the problem is that the tag sequence shall be just 17bp and the remaining sequences doesn't seem to match the adapter 1.
    anyone knows how to get the correct tag sequences from the sample fastq above?

    many thanks!

  • #2
    Did you try fastx_toolkit? It contains a script fastx_clipper that identify the 3'adapter and remove it. It allows for some mismatches and should correspond to what you're looking for.

    Comment


    • #3
      thanks for the recommendation and I will try it

      Comment


      • #4
        I found this only yesterday - really nice tool:

        Comment


        • #5
          Cutadapt

          I have used Cutadapt (code.google.com/p/cutadapt/). I liked this tool as it allows user to define and fine tune each of the parametre. You can also allow errors in identifying the adapters. If in case you want to check the 5' adapters, this will be a tool of choice as you can specify where to search the adapter (3' or 5' or anywhere).

          Comment


          • #6
            thanks for the reply and I will try them first and see how things going

            Comment


            • #7
              Biopieces got find_adaptor which allows removal of partial adaptor sequence:

              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, 03-27-2024, 06:37 PM
              0 responses
              12 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-27-2024, 06:07 PM
              0 responses
              11 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              53 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X