![]() |
|
![]() |
||||
Thread | Thread Starter | Forum | Replies | Last Post |
Colorspace bis-seq data analysis on Solid | Blaize | Epigenetics | 4 | 11-26-2013 01:36 AM |
question about Solid data analysis using bowtie? | wangleibio | RNA Sequencing | 5 | 03-26-2013 07:32 AM |
75+35 Pair-end SOLiD RNA-seq data analysis | endether | SOLiD | 11 | 12-12-2012 05:40 PM |
SOLiD data analysis with lifescope | lre1234 | Bioinformatics | 3 | 08-10-2012 05:39 AM |
![]() |
|
Thread Tools |
![]() |
#1 |
Member
Location: GZ,China Join Date: Jun 2014
Posts: 42
|
![]()
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.
mate1: @SRR586064.1 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/1 T30..01121.12.1032100213131122200031222022101302313 + !AB!!?:>@<!@B!;AB?AA@@<2<@?@@<?AB>A?9?:;@@>;-=>>7=@ @SRR586064.2 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_137/1 T00..00000.00.0000000002220301333000020000303000000 + !<B!!97=<A!<@!?>7?@;9+%+2%%-&-%%+6(,0*)3((%<%4.+8.1 mate2: @SRR586064.1 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/2 G10330000122222033220201000000220002000000000000000 + !@BBABBBB@>?@@(.))35.%-.3((%1+%((82-'.*-*/3*14*'696 @SRR586064.2 ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_137/2 G01002233300021321333003300011021333000110330003000 + !AA>>@A@?3=?:1+6@:?+ ![]() 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? |
![]() |
![]() |
![]() |
#2 |
Super Moderator
Location: Walnut Creek, CA Join Date: Jan 2014
Posts: 2,707
|
![]()
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. |
![]() |
![]() |
![]() |
#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:
Quote:
Quote:
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. |
||
![]() |
![]() |
![]() |
#4 | |
Super Moderator
Location: Walnut Creek, CA Join Date: Jan 2014
Posts: 2,707
|
![]() Quote:
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. |
|
![]() |
![]() |
![]() |
Tags |
solid data analysis |
Thread Tools | |
|
|