Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cufflinks non-model organism, issues with -b, and false concatenation of genes

    Hello,
    I have been working with the "tuxedo" package for a little while now, and have started getting the nice results that I want, but I still have a few nagging issues.

    One is that when I use the -b option, for multi-read correction in cuffdiff, I get a segmentation fault at differing stages of the run, and thus no result. If I do not use this option, I basically get no results, and the gene_exp.diff is basically full of NOTEST and LOWDATA entries.

    This is only an issue for the newest (and unfortunately much better) annotation and assembly, as when I run the package with the older files, it works generally fine (also with the -b option).

    Is there anything in the genome fasta or bowtie mapping files that I should look for in order to fix this problem? If anyone wants to take a look, I would be more than happy to send the files...

    Another issue I have is that at some point some clearly distinct genes are merged into one cufflinks transcript, so that in the gene_exp.diff file, an entry in the "gene" column would look like: Nasvi2EG000144,Nasvi2EG000145,Nasvi2EG000147,Nasvi2EG000149,Nasvi2EG000151 It is clear to me that I am losing quite some differential expression information due to this issue, and was wondering if there was a way to avoid it....

  • #2
    Are you using the 2.0.1 or 2.0.0 version? These issues are supposed to be fixed in that latest version. Another thing, -b is not multi-read-correction, it is frag-bias-correct.

    Comment


    • #3
      Originally posted by glados View Post
      Are you using the 2.0.1 or 2.0.0 version? These issues are supposed to be fixed in that latest version. Another thing, -b is not multi-read-correction, it is frag-bias-correct.
      This was in 2.0.1, as well as in earlier versions.
      Of course you are right about -b, I thought I had fixed it, but at least I got it right in the tags

      Comment


      • #4
        Ok. Then I don't know. Hopefully someone else do.

        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, 05-24-2024, 07:15 AM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 10:28 AM
        0 responses
        18 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 07:35 AM
        0 responses
        22 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-22-2024, 02:06 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Working...
        X