# What is this 5-column sequencing format from 2009?

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:

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?