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@:?+;A+0+921:-:B78'6?(/5/?5:26=&*
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?
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@:?+;A+0+921:-:B78'6?(/5/?5:26=&*
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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