Hi, everyone. I have ask this question on SEQanswers forum.
I want to do the mapping about AB SOLID data. They are paired-end sequencing. The format of .fastq files show below:
@SRR586064.1ugc_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=@
@SRR586064.1ugc_357_358_MatePair_2x50bp_solid0032_20100528_MP_ugc_357_854_13_97/2 G10330000122222033220201000000220002000000000000000 + !@BBABBBB@>?@@(.))35.%-.3((%1+%((82-'.*-*/3*14*'696
I try use the tool:SHRiMP2, but it is not friendly to solve my datasets. I run the command:
gmapper-cs -1 pair1.fastq -2 pair2.fastq -L ./test/Sscro --pair-mode opp-in -Q --trim-first --qv-offset 33 >pair12.sam 2>pair12.log
And I got the info in the end of file .log:
note: detected fastq format in input file [pair1.fastq] - Processing read files [pair1.fastq , pair2.fastq] note: quality value format not set explicitly; using PHRED+33 done r/hr r/core-hr There has been a problem reading in the read "SRR586064.1", the quality length exceeds the sequence length! Are you using the right executable? gmapper-cs for color space? and gmapper-ls for letter space?
I have tried some parameters of SHRiMP2, but failed. And I can't find any similar example from SHRiMP2 website. Does anybody get the same problem and have you solve it ? Or maybe I should use another tool, any suggestion?