Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Blast2go input files

    Hi everyone,

    I have a question regarding the options for blast2go input. I am currently analyzing an RNAseq project comparing gene expression patterns during four treatments, each with three biological replicates. I am using the Tuxedo suite (TopHat, Cufflinks, Cuffmerge, Cuffdiff) for assembly and differential expression analysis and I would like to look at the ontology of the differentially expressed genes that I was able to pull out from the cuffdiff output, but it doesn't seem to be in a format that blast2go can deal with. Has anyone else run into a similar issue? And if so, how do I go about getting my GO data for these genes? Is a file format change necessary, or am I missing something?

    Thanks,
    Alex

  • #2
    Blast2GO just needs a FASTA file of your gene sequences (one record per gene), or a BLAST XML file of your genes searched against the NCBI NR database.

    Comment


    • #3
      Originally posted by maubp View Post
      Blast2GO just needs a FASTA file of your gene sequences (one record per gene), or a BLAST XML file of your genes searched against the NCBI NR database.
      Thanks for the input. I am aware that a FASTA file is required for blast2go, but I am primarily interested in annotating only the transcripts that were differentially expressed among the treatment groups. Since that information in contained in the cuffdiff output, I'm curious if there is a way to generate a fasta file that contains only those sequences of interest.

      Thanks again,
      Alex

      Comment


      • #4
        In that case just filter your FASTA file of all genes to make a new smaller FASTA file of just the genes of interest (using the differentially expressed gene ID list from cuffdiff). That should be trivial in your scripting language of choice.

        Comment


        • #5
          Blast2GO has a GO term enrichment function, that might be what you want. You need a Blast2GO result for all sequences then give the test set as a list of sequence names that is then compared against all the sequences.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM
          • seqadmin
            Recent Advances in Sequencing Analysis Tools
            by seqadmin


            The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
            05-06-2024, 07:48 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 01:32 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-24-2024, 07:15 AM
          0 responses
          199 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 10:28 AM
          0 responses
          221 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 07:35 AM
          0 responses
          232 views
          0 likes
          Last Post seqadmin  
          Working...
          X