Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Creating Transcriptome File for Use With BWA from GTF file and genomic fasta file

    I downloaded the Mus musculus mm10 pre-built tophat indices from the Tophat website (http://ccb.jhu.edu/software/tophat/igenomes.shtml). This package comes with a .gtf file that specifies junction boundaries and start/stop codon positions. It also contains a .fa file for the mouse genome.

    I would like to produce a .fa file that contains all of the mouse RNA transcript sequences from the above two files. Is there any software that does this? I have read of de novo transcriptome assembly software like Trinity, but I do not think it would be ideal for what I would like to do here. I merely need some kind of script/tool to generate the annotated mRNA (and ideally, rRNA, mtRNA, and ncRNA) sequences that will match the annotation in the aforementioned two files (.gtf and .fa from the tophat pre-built index).

    Thank you kindly for your time and help. Please let me know if there is any further information you would like to help evaluate my query. If I do find an appropriate tool for this problem, I plan on writing a script to extract and splice necessary sequences from the genomic .fa file, and will upload this script for others to use (but would rather avoid re-inventing the wheel if possible!).

  • #2
    Hi
    Any solution of your problem ?
    I am confused with too

    Comment


    • #3
      Whenever I heard the word "gtf" or "vcf" then my mind goes to BEDtools. And indeed one of the programs is "fastaFromBed" which "Creates FASTA sequences based on intervals in a BED/GFF/VCF file." GTF is just a GFF in disguise.

      Comment


      • #4
        Thanks westerman, however, I like to ask you something different but relative.
        After running Denovo Trinity reports Trinity.fasta and then I did blast got blastx.outfmt6. I also have TransDecoder output i.e. Trinity.fasta.transdecoder.cds , Trinity.fasta.transdecoder.gff3 , Trinity.fasta.transdecoder.mRNA , Trinity.fasta.transdecoder.pep

        I am confused how to add real gene names in to Trinity.fasta So that Trinity numbered genes (TR1...n) will be replaced by real gene names which are available in Trinity.fasta.transdecoder.gff3 or blastx.outfmt6 ?
        Any idea ?

        Comment


        • #5
          Originally posted by jp. View Post
          Thanks westerman, however, I like to ask you something different but relative.
          After running Denovo Trinity reports Trinity.fasta and then I did blast got blastx.outfmt6. I also have TransDecoder output i.e. Trinity.fasta.transdecoder.cds , Trinity.fasta.transdecoder.gff3 , Trinity.fasta.transdecoder.mRNA , Trinity.fasta.transdecoder.pep

          I am confused how to add real gene names in to Trinity.fasta So that Trinity numbered genes (TR1...n) will be replaced by real gene names which are available in Trinity.fasta.transdecoder.gff3 or blastx.outfmt6 ?
          Any idea ?
          No idea. This is processing step that I do not use thus am unable to give advice.

          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