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:
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:
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
When I use srf_dump_all, the results look like this:
Code:
[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 ...
So, I ran it with srf2fasta, and the result looked like this:
Code:
>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 ...
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
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