Output file formats

[cgb]

the sig2 files are processed "traces" you can draw a bar chart with them for each sequence. The seq files are the final data - its trivial to convert the seq and prb files into a fastq file - there are tools floating around to do this.

generally the key is the first 4 columns : lane, tiles, x, y for the given cluster that gave the sequence.

[rebrendi]

Thank you very much, ECO!

So, I still need answers to the two other file formats, and the program to read them under windows (if it exists). I wonder, is it possible to extract the nucleotide numbers in the genome from these short raw data? And there are also other tags encoded somewhere in these files.

[ECO]

Hey Rebrendi, I fully expect someone more knowledgeable than myself will chime in soon, but I do know that the PRB file is the per base quality file. There is more info here:

For the latter one, four numbers per base are listed to present the negative log-transform of the probabilities of four nucleotides (A, C, G, T) to be sequenced at this base position.

...from http://rulai.cshl.edu/rmap/

So it's possible to use the PRB as the sequence as well.

Hopefully that will tide you over until said smarter person appears!

[rebrendi]

Hello,

Could you please help me to sort out with the output file formats?
What each column means, and which program (under Windows) to use to read these files?

Thank you very much!

(There are three output files,
First file has a name like s_2_0001_seq.txt and looks like this:

2 1 912 885 TGGCAAGGAAAATAAAATCAAAAA
2 1 901 884 TGGTACATATACACCATGAAATAT
2 1 897 115 TGAAGGACCAGAGTGCCTGGACTT
2 1 933 879 AAGGCAACAAAAAGAGACTCCATA
2 1 888 104 TGGGACACATTTAAAGCAACGAGA
2 1 920 116 AATCCAGAAGTGGGGGCCTGTGCA
2 1 920 894 TCAAAACTGAAACACTTCCCATCA
2 1 900 896 TGTCATCCTGAAGTGCAGTGGATA
2 1 896 921 TTAGGAAAAAACAAAAAACAAAAA
2 1 886 105 AGGGAAAATGGAAAAATAACAAAC
2 1 876 955 TACCAAACATTTGAGGCAGAAATG


Second file is named as s_2_0001_sig2.txt and looks like this:


2 1 912 885 2925.5 5978.4 913.5 6583.8 1032.0 1638.7 4854.6 221.5 109.3 1888.1 2405.1 2398.7 1271.8 4134.4 737.4 -222.2 2190.1 1825.4 679.2 -2.1 3953.1 277.9 391.4 334.6 1393.2 972.6 3596.5 1032.0 391.4 53.5 2777.0 -167.5 2737.7 277.9 913.5 109.3 2584.9 2398.7 334.6 109.3 2628.7 972.6 448.5 -57.4 2157.6 -705.0 165.3 1700.7 277.9 1091.6 448.5 1819.4 3357.7 -2.1 -2.1 1762.9 2325.5 277.9 1271.8 -222.2 1105.7 1032.0 109.3 109.3 2815.2 -112.5 391.4 1211.5 277.9 334.6 1151.4 1263.3 913.5 1464.4 505.9 165.3 2341.2 505.9 165.3 165.3 2221.7 -492.5 221.5 -112.5 1853.9 505.9 109.3 1393.2 492.8 165.3 448.5 165.3 1906.0 53.5 563.4 563.4

And the third file is named like s_2_0001_prb.txt, and looks like this:

-40 -5 -40 5 -40 -40 40 -40 -40 -40 1 -1 -40 40 -40 -40 13 -13 -40 -40 40 -40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 40 -40 -40 -40 6 -6 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 40 -40 -40 -40 2 -2 -40 -40 40 -40 -40 -40 -40 -40 -19 19 -19 19 -40 -40 40 -40 -40 -40 40 -40 -40 -40 18 -31 -40 -18 0 -10 -2 -22 40 -40 -40 -40
-40 -40 -40 40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 40 -40 -40 -40 40 -40 -40 -40 -40 -40 -40 40 40 -40 -40 -40 -40 -40 -40 40
-40 -40 -40 40 -40 -40 40 -40 40 -40 -40 -40 40