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Old 12-22-2011, 08:42 AM   #61
Rick Westerman
Location: Purdue University, Indiana, USA

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Originally Posted by doctortrout View Post
This newbie will use the color sequence you entered is a good example of why the color scheme depicted in Fig 5 cannot be correct.

RRGBGYY can indicate either the base sequence you show: ATACCATC or the sequence CGCAACTC.
Not at all. The initial base *must* be an 'A' because that is what I defined it as. Once you have the initial base then the rest follows unambiguously. I gave you aRRGBGYY with the small 'a' representing the initial starting base of 'A'. I did not give you an unattached 'RRGBGYY'.

You have the correct underlying idea that color-space can be ambiguous if you start off with no-predefined starting base or if you go 'off-frame'. But when working with color-space you always either (1) start with a pre-defined base or (2) do mapping, in color-space, against a reference thus keeping yourself 'in-frame'.

The above is why everyone says "do work in color-space when you have color-space reads; do not translate into base-space as your initial step." See the many postings on SeqAnswers in regards to this.
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Old 12-22-2011, 08:49 AM   #62
Rick Westerman
Location: Purdue University, Indiana, USA

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I should point out that the very first dinuc in the columns under 'Template Sequence' in figure 5 is incorrect. It should be 'AT' instead of 'TA'. Looking at the '1st base vs. 2nd base' diagram to the left of 'Template Sequence' shows this.
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Old 06-09-2012, 02:52 AM   #63
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can you tell me why probes has 8 nucleotides? what´s a function of non-coding bases? thanks
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Old 06-09-2012, 07:24 AM   #64
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ligase binding is most efficient at 8 bases. So you need 8mer probe.
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Old 07-16-2012, 10:04 AM   #65
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Default SOLiD quality data box-plots.... strange?

hi everyone,
I have used the to change the csfasta and qual files to standard fastq files.
I then ran fastqc to view boxplots of quality data and got these results, attached.
They seem to have poor quality every 5 nt, as if the primer 5 of the procedure failed....
Has anyone seen this type of quality plots before???
I am new with solid data, have worked with ilumina and 454 before.
Thanks for any guidance in advance.
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File Type: png per_base_quality.png (15.6 KB, 14 views)
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Old 07-24-2012, 05:51 AM   #66
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Default which adapter to start sequencing, P1 or P2 primer?


I'm using SOLiD SAGE. The SAGE method seems to preserve the strand information. The only unclear question is which primer (or adapter) SOLiD uses to start the sequence. According to the chemistry, it is likely the P1 primer and reading from 3' to 5'. Can anyone confirm it?
I stuck with this for a long time, hopefully someone can have an answer,

Thanks so much,
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Old 12-12-2012, 04:37 PM   #67
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I'm analyzing a "second-hand" dataset generated using SOLiD 4. It is a transcriptome mate pair library that is 52 x 37 nt, and I cannot for the sake of me find the protocol that was used to generate those specific read lengths. I have F3 and R3 reads, so I am assuming it is a circularization protocol, but I do not know what the size selection parameters were, or how the circles were cut to produce the final fragments. This info would be very valuable for a more accurate mapping.

Any knowledge would be greatly appreciated!

Thanks a lot,

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Old 04-23-2013, 03:07 PM   #68
shahinda rezk
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Default SOLiD

please i want to know which base shall i know to begin translating the colours to base sequence?
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