text: user292: There is high throughput sequencing data here, and I don't know what format it is in.
  It was submitted in 2009, and the description says the following:
  
  Library strategy:     ncRNA-Seq
  Library source:   transcriptomic
  Library selection:    size fractionation
  Instrument model:     Illumina Genome Analyzer II
  Description:  CIPPNK, tar file of Illumina *_seq.txt files provided as supplementary file
  
  I got the archive here:
  ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455387/suppl/GSM455387%5FWT%5FCIPPNK%5Fseq%5Fs1%2Etar%2Egz
  Inside, there are 330 files from s_1_0001_seq.txt to s_1_0330_seq.txt which are tab-delimited text files where the first column is always 1, the second has the number found in the file name, then 2 mysterious integers, and then what looks like a read of length 36, with sometimes a dot instead of a letter:
  $ head s_1_0330_seq.txt 
  1   330 690 785 TTCCTACATTGTTCCCCCATGCTGTTGGCACCATCA
  1   330 44  145 TTTTTATCACGAGTTTTAAATCTGTAGTCACCATCA
  1   330 53  141 AATAATGCATAACAAAACGGAATCTGTAGAA.AAA.
  1   330 784 461 TAATTGTAGTGATTGATCAATCTGTAGGCACCATCA
  1   330 588 634 TATTATGCACATTTTCTAGTTCACTGTAGGCACCAT
  1   330 718 678 TTACATGTTTCGGGTAGGAGCCTGTAGGCACCATCA
  1   330 635 834 TGTGATCATTAGTTCAAAGCCCCCTGTCGGCACCCT
  1   330 494 523 TGAAAATCAAAAATGCTGAACTGTAGGCACCATCAA
  1   330 393 783 TTTTTTTTTAAATTTAAAAAAACTGTAGGCACCATC
  1   330 48  148 GTTTAACCGTGTAGACGTTGGTTTCTGTAGGCACCA
  
  This seems to be some "old" high-throughput sequencing format. I think someone in a 2008 message in sequanswers was dealing with this type of file:
  http://seqanswers.com/forums/showpost.php?p=1841&postcount=8
  What is this format that seemed so standard back then, that the authors did not give more info than describing the files as "Illumina *_seq.txt files"? I do not dare ask them for such a trivial question (the given contact is a Nobel prize laureate and is probably too busy to answer random bioinformatics questions).
  In particular, what are the columns 3 and 4, and what do the dots mean?
  
  user964: This is an early Solexa/Illumina sequencer format. The columns are the identifier to location on the flowcell.  I believe the "." was the original placeholder for an unread base, which has been replaced by and "N" in current Illumina sequencing output.
  From on http://www.crg.eu/en/content/processing-and-analysis-illumina-sequencing-data.
  
  seq.txt (Gerald)
  4 1 23 1566 ACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCG
  The first 4 columns are an ID that provides location details of the cluster in the flow cell, followed by the read sequence. Seq.txt file size typically ranges between 250 Megabytes and 1 Gigabyte. One file is generated per lane.
  
  
original_text: 292: <p>There is high throughput sequencing data <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM455387" rel="nofollow noreferrer">here</a>, and I don't know what format it is in.</p>
  
  <p>It was submitted in 2009, and the description says the following:</p>
  
  <ul>
  <li><p>Library strategy:     ncRNA-Seq</p></li>
  <li><p>Library source:   transcriptomic</p></li>
  <li><p>Library selection:    size fractionation</p></li>
  <li><p>Instrument model:     Illumina Genome Analyzer II</p></li>
  <li><p>Description:  CIPPNK, tar file of Illumina *_seq.txt files provided as supplementary file</p></li>
  </ul>
  
  <p>I got the archive here:</p>
  
  <p><a href="ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455387/suppl/GSM455387%5FWT%5FCIPPNK%5Fseq%5Fs1%2Etar%2Egz" rel="nofollow noreferrer">ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455387/suppl/GSM455387%5FWT%5FCIPPNK%5Fseq%5Fs1%2Etar%2Egz</a></p>
  
  <p>Inside, there are 330 files from <code>s_1_0001_seq.txt</code> to <code>s_1_0330_seq.txt</code> which are tab-delimited text files where the first column is always <code>1</code>, the second has the number found in the file name, then 2 mysterious integers, and then what looks like a read of length 36, with sometimes a dot instead of a letter:</p>
  
  <pre><code>$ head s_1_0330_seq.txt 
  1   330 690 785 TTCCTACATTGTTCCCCCATGCTGTTGGCACCATCA
  1   330 44  145 TTTTTATCACGAGTTTTAAATCTGTAGTCACCATCA
  1   330 53  141 AATAATGCATAACAAAACGGAATCTGTAGAA.AAA.
  1   330 784 461 TAATTGTAGTGATTGATCAATCTGTAGGCACCATCA
  1   330 588 634 TATTATGCACATTTTCTAGTTCACTGTAGGCACCAT
  1   330 718 678 TTACATGTTTCGGGTAGGAGCCTGTAGGCACCATCA
  1   330 635 834 TGTGATCATTAGTTCAAAGCCCCCTGTCGGCACCCT
  1   330 494 523 TGAAAATCAAAAATGCTGAACTGTAGGCACCATCAA
  1   330 393 783 TTTTTTTTTAAATTTAAAAAAACTGTAGGCACCATC
  1   330 48  148 GTTTAACCGTGTAGACGTTGGTTTCTGTAGGCACCA
  </code></pre>
  
  <p>This seems to be some "old" high-throughput sequencing format. I think someone <a href="http://seqanswers.com/forums/showthread.php?t=282" rel="nofollow noreferrer">in a 2008 message in sequanswers</a> was dealing with this type of file:</p>
  
  <p><a href="http://seqanswers.com/forums/showpost.php?p=1841&amp;postcount=8" rel="nofollow noreferrer">http://seqanswers.com/forums/showpost.php?p=1841&amp;postcount=8</a></p>
  
  <p>What is this format that seemed so standard back then, that the authors did not give more info than describing the files as "Illumina *_seq.txt files"? I do not dare ask them for such a trivial question (the given contact is a Nobel prize laureate and is probably too busy to answer random bioinformatics questions).</p>
  
  <p><strong>In particular, what are the columns 3 and 4, and what do the dots mean?</strong></p>
   964: <p>This is an early Solexa/Illumina sequencer format. The columns are the identifier to location on the flowcell.  I believe the &quot;.&quot; was the original placeholder for an unread base, which has been replaced by and &quot;N&quot; in current Illumina sequencing output.</p>
  <p>From on <a href="http://www.crg.eu/en/content/processing-and-analysis-illumina-sequencing-data" rel="noreferrer">http://www.crg.eu/en/content/processing-and-analysis-illumina-sequencing-data</a>.</p>
  <blockquote>
  <p>seq.txt (Gerald)</p>
  <p>4 1 23 1566 ACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCG</p>
  <p>The first 4 columns are an ID that provides location details of the cluster in the flow cell, followed by the read sequence. Seq.txt file size typically ranges between 250 Megabytes and 1 Gigabyte. One file is generated per lane.</p>
  </blockquote>
  