Hi, I'm getting a error name base quality out of range . while aligning my reads using Novoalign.
Command used for aligning
novoalign -d Reference/Novoalign/hg37.nix -f data/SRR504483_1.fastq data/SRR504483_2.fastq -i 200,50 -o SAM
Error message
Error: Base quality out of range for file format. Please specify file format with -F option.
@SRR504483.1.1 HWI-ST423:183:C03RLACXX:3:1101:1425:2052 length=101
NAAGGTGGCTGAGCCTGCAGGGAGTCCTTAGGAAAAGGGTGAGAAGACCTTGATAGGCCTGACTGTGTAAAGATGTAGCTTGGCNNNNNNNNNNNNNNNNN
+
MYb
abdddcdfffffffffffffffffffbceedefdedeeeffefffeefeffcfefefcdddddbb`aabaaaaaaa``
I also downloaded SRR504483 from the short read archive and the first read is
@SRR504483.1 HWI-ST423:183:C03RLACXX:3:1101:1425:2052 length=101
NAAGGTGGCTGAGCCTGCAGGGAGTCCTTAGGAAAAGGGTGAGAAGACCTTGATAGGCCTGACTGTGTAAAGATGTAGCTTGGCNNNNNNNNNNNNNNNNN
+
#1=DFDEFHHHGHJJJJJJJJJJJJJJJJJJJFGIIHIJHIHIIIJJIJJJIIJIJJGJIJIJGHHHHHFFDEEFEEEEEEEDD#################
It looks like your reads may have had some process run on them to change the quality coding. The original qualities work.
Thanks for your reply i sorted the problem with the read wile downloading the file using fastq-dump i set the quality as 30 that's why i faced the problem.