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Old 07-23-2014, 12:40 AM   #1
Lv Ray
Location: GZ,China

Join Date: Jun 2014
Posts: 42
Post Puzzling to SOLID data analysis

Can anyone help me about the SOLID 4 sequencing data ? I got them from SRA database. And they seems have been treated. they are mate paired data.
@SRR586064.1 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/1
@SRR586064.2 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_137/1

@SRR586064.1 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/2
@SRR586064.2 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_137/2

MY questions are:
1)what is the first read in mate1?(some like the first read have the symbol . ,what does it mean?) But in mate1 ,there are many reads like mate2.
2) can I convert the SOLID fastq(color space) to necleotide space? Anything lose?
3) If I convert the color space field, how about the QV lines?
4) I am similar to Bowtie2, can I use it to do mapping?
5)last, should I do the QC before conversion or after?
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Old 07-23-2014, 09:07 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

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1a) The first read is "T30..01121.12.1032100213131122200031222022101302313". The reads are a single letter followed by numbers.
1b) '.' means 'N' (a no-call).
2) Not without mapping. Only mapped reads can be correctly translated to base-space.
3) The QV lines can be sort of interpolated by averaging adjacent values.
4) You need to map with a colorspace-aware aligner. I'm pretty sure BWA allows this.
5) QC must be done before mapping.
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Old 07-23-2014, 11:38 AM   #3
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

Actually Brian is wrong about #2. It is quite trivial to convert from color-space to base-space without mapping. I use to be able to do so by hand -- just for mental exercise -- when we owned a SOLiD. For example your read:
converts into:
[BTW: I see that Wikipedia says "... There is one unambiguous conversion of a base reference sequence into color-space, but there are four possible conversions of a color string into base strings" which is wrong. I should pull out my old conversion table and correct this.]

That said it is quite dangerous to rely on the conversion from color-space to base-space. If there is any uncertainty in the color-space then the probability of going off-track in base-space is high with the consequent corruption of your base-space data. Mapping the (older SOLiD generated) read to a known reference is the way to keep the corruption from occurring.

Color-space can be a very powerful self-correcting format <em>as long as you remain in color space</em>. Do not convert from color-space into base-space until you are completely done with your analysis.

BWA dropped support of color-space as of version 0.6 so you will have to use an older version.

Bowtie2 never supported color-space although the former program Bowtie does.

BTW: Not that this help you but the new SOLiD has a self-correcting method which re-aligns the read properly ever fifth base.
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Old 07-23-2014, 12:51 PM   #4
Brian Bushnell
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Originally Posted by westerman View Post
Actually Brian is wrong about #2. It is quite trivial to convert from color-space to base-space without mapping.
I wouldn't say "wrong"... though maybe misleading. It is impossible to correctly translate an imperfect colorspace read to base-space without mapping. And since SOLiD has an extremely high error rate - a minority, maybe around 20%, of reads were error-free in the SOLiD 4 data I've processed - in practice, it's not a useful thing to do. And indeed it is completely impossible to translate a read with a no-called base, before mapping.

It's also not possible to unambiguously translate a colorspace read to base-space even AFTER mapping; the translation requires assumptions about the probability of errors versus SNPs versus indels and the results are highly subjective.
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