I am working with some Illumina sequences and I have some doubts. Could someone help me, please? This sequences are from Hi-Seq 2000 but it was run in 2010.
I am not sure if it is single or paired end. How can I check that?
I am trimming it using trimmomatic
trimmomatic SE -threads 10 -phred64 \ ../../rawdata/BRS_I24.fastq \ BRS_I24_trim.fastq \ ILLUMINACLIP:/data/apps/trimmomatic/0.36/adapters/TruSeq2-SE.fa:2:30:10 \ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36
-However, in that time. Illumina had changed the type of quality score and then later the got back to the old one, I don´t know which one should I use. If is it the -phred64 or -phred33? The quality score looks like this:
@HWI-ST365_0091:2:1:1192:1999#TGTCAT/1 CCTGCTCTAAATGCTTCTATTTGCCGCATGATTCCAGTCTTGACAGTTGCATCTGCCACCAAGGATATATACTCCTCCAAATTGTTGATATCAACAATT +HWI-ST365_0091:2:1:1192:1999#TGTCAT/1 YXYY[[X[[cccccccccccccccccccc_____c__ccccc_c[cccZccccccZccccc\_c[\]]Z]YYYY[ZXXRYYY]V[[[[XSUSUUXXXRZ
-Also I was seeing that when the sequencing is from GA II it is better to use TruSeq2-SE.fa:2:30:10, while with Hiseq it is better use TruSeq3-SE.fa:2:30:10. Is that right? I know the the sequencing kit used was TruSeq(TM) SBS v5.
Thanks in advance