how to do alignment for SOLiD data

bobo xin · 08-01-2011, 02:34 AM

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

nilshomer · 08-01-2011, 08:28 AM

Please do not post your question in multiple places. Also try searching the forums for your answer before posting.

bobo xin · 08-01-2011, 05:58 PM

Quote:

Originally Posted by nilshomer

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.

samanta · 08-01-2011, 06:32 PM

Quote:

Originally Posted by bobo xin

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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08-01-2011, 02:34 AM	#1
bobo xin Junior Member Location: shenzhen china Join Date: Jul 2011 Posts: 7	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

08-01-2011, 08:28 AM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Please do not post your question in multiple places. Also try searching the forums for your answer before posting.