Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • current version of tbl2asn for linux

    Hi,

    I am trying to create an .sql file to upload it at NCBI TSA database. My input is a de novo assembly of approx. 20 000 contigs as .fsa. From the NCBI webpage I got the information that I should use tbl2asn for this.

    Now I got the error: "This copy of tbl2asn is more than one year old. Please download the current version."

    My output is empty and I don't get a different error massage.

    I cannot find something else than the 14.3 release in the FTP directory of NCBI, but the instruction say one should use higher than 19.3.

    Heeeelp,

    anna.

  • #2
    I am relpying to my own post:

    I think the old version of tbl2asn is not the problem. Instead:

    The TSA NCBI page says I should include an assembly.cmt file with the argument -w assembly.cmt. As soon as I write this in the command tbl2asn doesn't do anything anymore.

    Is there somebody who already submitted a batch-file to TSA (transcriptome sequence assembly) database and who used tbl2asn for this?

    Can anybody tell me why there is no -w argument in the documentation of tbl2asn but at the TSA information page?

    Comment


    • #3
      I have the same problem. I have downloaded the newest version (14-06-2012) of the NCBI website, and still I get an error.
      Can someone help us?

      Comment


      • #4
        I don't know if you have the same problem than me. I could solve my problem finally by specifying the molecule type, the technique and the BioProject in the defline of the fasta file. Your fasta should lok like that:

        >contig01256 [tech=TSA] [moltype=mRNA] [bioproject=PRJNA159263]
        CGTCGTGACCTTGGCTGTCACTCAACCTCTCAATGTAGCAGCCCACTGACGAGAAAGCAA
        CATACCACAAGTATCAAGAACATCTATAACTATCACATCCATGGTCAAATGGATATCCGG
        ATACATTGATAAGCTGACTTGAAGGTTCAAGATTACTCCTACCACATCAATTTCTCTTGA
        ATCCATGGCACAAACATTGT
        >contig12463 [tech=TSA] [moltype=mRNA] [bioproject=PRJNA159263]
        ATGTGGAAAAAGCAACTGCGGCAGGGTTGGATGCAATCATTATTAAAGGTGTTGAAGTAG
        GTGGTTATGTCATTCCCAAGGTTGAAaGGaTAGATTACCCATTTTAAAAaCGtGGAGAAG
        TAATCTAGCCTATTGTATGTAAGAaTATATACTAATAAaGGATTgaCAAGAaGTGTAGAG
        CCGaCcAACATGGAATCTAT

        regards,

        anna

        Comment


        • #5
          This problem is still going on. I have it now and followed your advice but it did not work... e.g.

          tbl2asn -p 2882.fsa -t template.sbt -a s -j "[organism=Listeria monocytogenes]" -w comment.txt -y "[tech=MiSeq] [moltype=DNA] [bioproject=PRJNA320339]" -j "[organism=Listeria monocytogenes] [strain=2882.fsa]"

          [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.

          But I have the current version from ftp.

          S.

          Comment


          • #6
            This problem is still going on. I have it now and followed your advice but it did not work... e.g.

            tbl2asn -p 2882.fsa -t template.sbt -a s -j "[organism=Listeria monocytogenes]" -w comment.txt -y "[tech=MiSeq] [moltype=DNA] [bioproject=PRJNA320339]" -j "[organism=Listeria monocytogenes] [strain=2882.fsa]"

            [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.

            But I have the current version from ftp.

            edit> I ahve realised that the command only accepts a folder of sequences for -p, not a single file.. put you data for each sample in a separate folder.

            S.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Recent Advances in Sequencing Technologies
              by seqadmin







              Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

              Long-Read Sequencing
              Long-read sequencing has...
              12-02-2024, 01:49 PM
            • seqadmin
              Genetic Variation in Immunogenetics and Antibody Diversity
              by seqadmin



              The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
              11-06-2024, 07:24 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 12-02-2024, 09:29 AM
            0 responses
            139 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 12-02-2024, 09:06 AM
            0 responses
            50 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 12-02-2024, 08:03 AM
            0 responses
            38 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 11-22-2024, 07:36 AM
            0 responses
            70 views
            0 likes
            Last Post seqadmin  
            Working...
            X