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Old 08-01-2011, 02:34 AM   #1
bobo xin
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Default how to do alignment for SOLiD data

hello all:
I will analysis the SOLiD sequence data ,but I don't know how to do alignment for these data.I konw bwa can do this ,but I don't konw how.
Anybody can tell me?
Thank you very much.

my data is .fq files, like this :
@SRR010454.1 VAB_Solid0100_20080703_1_Pilot2_YRI_Fragment_A_library13
T30030220303311000032221122100210000
+
!&+5,)%)9++'.//1$#;70)4+&)(%.6/(%<&2
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Old 08-01-2011, 08:28 AM   #2
nilshomer
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Please do not post your question in multiple places. Also try searching the forums for your answer before posting.
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Old 08-01-2011, 05:58 PM   #3
bobo xin
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Quote:
Originally Posted by nilshomer View Post
Please do not post your question in multiple places. Also try searching the forums for your answer before posting.
Sorry! I'm a rookie here.
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Old 08-01-2011, 06:32 PM   #4
samanta
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Quote:
Originally Posted by bobo xin View Post
hello all:
I will analysis the SOLiD sequence data ,but I don't know how to do alignment for these data.I konw bwa can do this ,but I don't konw how.
Anybody can tell me?
Thank you very much.

my data is .fq files, like this :
@SRR010454.1 VAB_Solid0100_20080703_1_Pilot2_YRI_Fragment_A_library13
T30030220303311000032221122100210000
+
!&+5,)%)9++'.//1$#;70)4+&)(%.6/(%<&2
Almost all alignment programs will work, but you have to use the programs in color space. If you do not understand color space, here is my introduction on how color space works (http://www.homolog.us/blogs/?p=27), but that is not the definitive document and you can find many others. On the sidebar of above link, I have a link for 'solid software tools' from ABI. That is the best place for you to start.
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