Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • s_*_export.txt VS s_*_sequence.txt

    Hi All,

    What's the relationship between the s_*_export.txt and s_*_sequence.txt ?

    I previously supposed the export file is the alignment of the sequence file, but the export file contains more reads than the sequence file.

    Then I supposed the sequence file is the filtered results based on the export file, and I counted the total number of unique hits, "N0:N1:N2", "NM" and "QC". There is no consistent sum among these numbers.

    Anybody knows the exact relationship between the two files?

    I appreciate any helps from you guys.

    Jiang
    Last edited by zhuj; 05-30-2010, 01:39 PM.

  • #2
    My guess would be that the sequence file contains only the sequences that passed the chastity filter while the xport file contains all reads. Could you check that by counting the number of 'Y's in the chastity column?

    Simon

    Comment


    • #3
      Simon is correct; the sequence file contains the reads that pass filter. Also, depending upon the configuration, the sequence file format can vary (options are fastq, fasta, or scarf).

      -Harold

      Comment


      • #4
        Yeah, the number of "Y" in the filtering column is the same as the number of reads in sequence file.

        Thanks Simon and Harold.

        Jiang

        Comment


        • #5
          I guess sequence file is consistent with *.sorted.txt file

          Comment


          • #6
            The sorted file contains those reads that pass the chastity filter AND uniquely align to the reference genome.

            -Harold

            Comment

            Latest Articles

            Collapse

            • 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
            • seqadmin
              The Impact of AI in Genomic Medicine
              by seqadmin



              Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
              02-26-2024, 02:07 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-14-2024, 06:13 AM
            0 responses
            33 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-08-2024, 08:03 AM
            0 responses
            72 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-07-2024, 08:13 AM
            0 responses
            80 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-06-2024, 09:51 AM
            0 responses
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X