Convert 0123 into nucleotides from a SOLiD srf file.

[shunyip]

I downloaded some .srf files from GEO, which are RNA-seq data. By using the Staden Package, I was able to do the followings

When I use srf_dump_all, the results look like this:

[Info]

[Trace]
VAB_ESC_A1.max2302_1929_1121_F3,1.4678048.1.50.38.3###

[Header]
7               # format
0               # NPoints
50              # NBases
0               # NFlows
0               # maxTraceVal
0               # baseline
0               # leftCutoff
51              # rightCutoff

[Bases]
0 00000 +00 +00 +00 +00 #  0
0 00001 +00 +00 +00 +00 #  1
2 00002 +00 +00 +00 +00 #  2
1 00003 +00 +00 +00 +00 #  3
1 00004 +00 +00 +00 +00 #  4
2 00005 +00 +00 +00 +00 #  5
0 00006 +00 +00 +00 +00 #  6
0 00007 +00 +00 +00 +00 #  7
1 00008 +00 +00 +00 +00 #  8
1 00009 +00 +00 +00 +00 #  9
3 00010 +00 +00 +00 +00 # 10
3 00011 +00 +00 +00 +00 # 11
0 00012 +00 +00 +00 +00 # 12
0 00013 +00 +00 +00 +00 # 13
1 00014 +00 +00 +00 +00 # 14
3 00015 +00 +00 +00 +00 # 15
3 00016 +00 +00 +00 +00 # 16
3 00017 +00 +00 +00 +00 # 17
2 00018 +00 +00 +00 +00 # 18

...

I understand that it probably means that there are no quality score, so I gave up on converting it into fastq.

So, I ran it with srf2fasta, and the result looked like this:

>VAB_ESC_A1.max502_1581_384_F3,1.-4766655.1.46.42.2###
01233303132002231201222021220313221233322222021122
>VAB_ESC_A1.max1676_1611_977_F3,1.4766656.1.46.46.0###
00203223332122313022120222102132200231303332120202
>VAB_ESC_A1.max1901_463_960_F3,1.4766656.1.46.46.0###
00203223332122313022120222102132200231303332120202
>VAB_ESC_A1.max2016_1623_357_F3,1.-4766656.1.46.44.1###
22123330313200223120122202122031322123332232202223
>VAB_ESC_A1.max1843_1702_1379_F3,1.4766657.1.46.46.0###
02032233321223130221202221021322002313033321202020
>VAB_ESC_A1.max1849_392_964_F3,1.4766658.1.44.44.0###
20322333212231302212022210213220023130333212220202
...

Now, I am wondering what do 0,1,2,3 represent.
In other words, does 0 mean A,C,G or T? and also does 1 mean A,C,G or T? and etc

Thank you for your help,
Ken

[mbblack]

You need to use abi-dump (see the NCBI documentation for the SRA tools) if you wish to properly convert srf files into color space read (csfasta files) and associated color space quality scores (csqual files).

You want to keep those files in color space if you plan to do anything with them.

Literally, a 0 means a blue color space read, a 1 means a green, a 3 means a yellow and a 4 means a red

see http://seqanswers.com/forums/showthread.php?t=10 for details on ABI color space sequence reads

You can also look at https://www.biostars.org/p/43855/ to explain SOLiD color coding in read files.