I am get Illumina sequecing reads from BGI.
They told me that the version is RTA 1.13.48 and the quality code is ASCII 66 to 105.
(a) According to the info I read for Wiki and others, generally there should be two types of quality coding for illumina: (1) ASCII 64 to 126; Illiumina 1.3+ (2) ASCII 33 to 126; Illumina 1.8+.
So, I am confused about which type of coding my data are? ASCII 64 or 33.
(b) I want to use BWA and SAMtools to analysis my data. I will do BWA first and then apply SAMtools to the output BAM file.
WBA's default setting is for ASCII 33, but the "-I" will allow data with ASCII 64.
I am wondering what option should I use?
Samtool's default is also for ASCII 33 (and "-6" in mpileup allow data with ASCII 64). I read some info show that BWA converts the SAM/BAM output to ASCII 33. So, I don't need to worry about the coding type for samtools analysis as long as the output is from BWA. Is that correct?
Thanks,
Chih
They told me that the version is RTA 1.13.48 and the quality code is ASCII 66 to 105.
(a) According to the info I read for Wiki and others, generally there should be two types of quality coding for illumina: (1) ASCII 64 to 126; Illiumina 1.3+ (2) ASCII 33 to 126; Illumina 1.8+.
So, I am confused about which type of coding my data are? ASCII 64 or 33.
(b) I want to use BWA and SAMtools to analysis my data. I will do BWA first and then apply SAMtools to the output BAM file.
WBA's default setting is for ASCII 33, but the "-I" will allow data with ASCII 64.
I am wondering what option should I use?
Samtool's default is also for ASCII 33 (and "-6" in mpileup allow data with ASCII 64). I read some info show that BWA converts the SAM/BAM output to ASCII 33. So, I don't need to worry about the coding type for samtools analysis as long as the output is from BWA. Is that correct?
Thanks,
Chih
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