FASTQ to FASTQSanger using Groomer question

[ykingh]

My data (paired end reads) come from Illumina Hiseq 2000 using multiplexed sequencing technology on Genome DNA seq. L6_R1 and L6_R2 is the pair from Lane 10. My data are as follows:

File L6-R1
@HWI-ST261:6:1:1385:2207#TAGCTT/1
GGTTCGCATTAC...............ATTCATTCCCTGAT..................TTAAACT.................TTGTCCTTCTCAACTTG
+
____`_```_W\BBBBBBBBBBBBBBBT\]\^^^^___`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

File L6_R2

@HWI-ST261:6:1:1663:2218#TAGCTT/2
TGAG.AAT....TTTCGGGTT.....AGTTTT.......TCTCTGGGATTAGGGTTTACGAGTACGTGGATAATGGG.......................
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB


I used FASTQ Groomer on data L6_R1 and L6_R2. I chose Illumina 1.3 + as the input quality scores type and I got the report as follows
Info: Groomed 118063852 illumina reads into sanger reads.
Based upon quality and sequence, the input data is valid for: None
Input ASCII range: 'B'(66) - 'h'(104)
Input decimal range: 2 - 40

Is it right for me to choose Illumina 1.3 + as Fastq data format?

[GenoMax]

Do you know what version of illumina pipeline was used to generate this data? If you do not know, it would be helpful to ask the folks who generated this data.

[swbarnes2]

That does look like Illumina 1.3 1.3 starts at ASCII 64, so @ is 0, and B is 2, which is really the lowest score, which is what you have there.

So that much you did correctly, but it looks like your data is very poor quality, maybe that's why its being rejected.