hello,
Please look at base quality string in my sample2New.fq file
@EBRI093151_0051:4:55:2998:9540#0/1
ACAACACAGTGGGTTGGAGTAGAGCATCTCCAAAGGCCCTTTCCAATCCAACATGAGTAACTCAAGCTCTGCACCAGCCACGAAAAGGCAAGGCTTTGGAT
+
FFFFFFFFFFDFFBFDEAEEEFFFFFFFFCFFEFFCEEEDDFFEEEFEADDFDFDEEDFFE@FCDDD>ACDFADD?CCECDB<?@047:9@?BB+B@@@]]
after commands
opt/bwa-0.6.2/bwa index -a bwtsw -p ref reference.fa
/opt/bwa-0.6.2/bwa aln -t 10 -f sample2New.sai -I ref sample2New.fq
/opt/bwa-0.6.2/bwa samse -f sample2New.sam -r "@RG\tID:sample2\tPL:ILLUMINA\tPUu1\tLB:sample2\tSM:sample2" ref sample2New.sai sample2New.fq
I can see changed base quality string in the sample2New.sam file
EBRI093151_0051:4:55:2998:9540#0 0 Chr10 377653 0 101M * 0 0 ACAACACAGTGGGTTGGAGTAGAGCATCTCCAAAGGCCCTTTCCAATCCAACATGAGTAACTCAAGCTCTGCACCAGCCACGAAAAGGCAAGGCTTTGGAT ''''''''''%''#'%&"&&&''''''''$''&''$&&&%%''&&&'&"%%'%'%&&%''&!'$%%%^_"$%'"%% $$&$%#^] !^Q^U^XESC^Z! ##^L#!!!>> RG:Z:sample2 XT:A:R NM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:101 XA:Z:Chr10,+33,101M,0;Chr10,+242847,101M,0;
and ofcourse the command
java -Xmx8g -jar /opt/picard-tools-1.85/SortSam.jar SO=coordinate INPUT=sample2New.sam OUTPUT=sample2New.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
fails with error
Exception in thread "main" java.lang.IllegalArgumentException: Invalid fastq character:
Why "bwa samse" is changing quality encoding??
Do you have an idea what Im doing wrong?
thanks
Please look at base quality string in my sample2New.fq file
@EBRI093151_0051:4:55:2998:9540#0/1
ACAACACAGTGGGTTGGAGTAGAGCATCTCCAAAGGCCCTTTCCAATCCAACATGAGTAACTCAAGCTCTGCACCAGCCACGAAAAGGCAAGGCTTTGGAT
+
FFFFFFFFFFDFFBFDEAEEEFFFFFFFFCFFEFFCEEEDDFFEEEFEADDFDFDEEDFFE@FCDDD>ACDFADD?CCECDB<?@047:9@?BB+B@@@]]
after commands
opt/bwa-0.6.2/bwa index -a bwtsw -p ref reference.fa
/opt/bwa-0.6.2/bwa aln -t 10 -f sample2New.sai -I ref sample2New.fq
/opt/bwa-0.6.2/bwa samse -f sample2New.sam -r "@RG\tID:sample2\tPL:ILLUMINA\tPUu1\tLB:sample2\tSM:sample2" ref sample2New.sai sample2New.fq
I can see changed base quality string in the sample2New.sam file
EBRI093151_0051:4:55:2998:9540#0 0 Chr10 377653 0 101M * 0 0 ACAACACAGTGGGTTGGAGTAGAGCATCTCCAAAGGCCCTTTCCAATCCAACATGAGTAACTCAAGCTCTGCACCAGCCACGAAAAGGCAAGGCTTTGGAT ''''''''''%''#'%&"&&&''''''''$''&''$&&&%%''&&&'&"%%'%'%&&%''&!'$%%%^_"$%'"%% $$&$%#^] !^Q^U^XESC^Z! ##^L#!!!>> RG:Z:sample2 XT:A:R NM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:101 XA:Z:Chr10,+33,101M,0;Chr10,+242847,101M,0;
and ofcourse the command
java -Xmx8g -jar /opt/picard-tools-1.85/SortSam.jar SO=coordinate INPUT=sample2New.sam OUTPUT=sample2New.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
fails with error
Exception in thread "main" java.lang.IllegalArgumentException: Invalid fastq character:
Why "bwa samse" is changing quality encoding??
Do you have an idea what Im doing wrong?
thanks
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