Error while aligning the sequence using Novoalign

Question

[manojkumarbioinfo]

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 + MYbabdddcdfffffffffffffffffffbceedefdedeeeffefffeefeffcfefefcdddddbb`aabaaaaaaa``

Answer 1

[Sparks]

The quality scores appear to be in old Solexa format which was 64+ 10log10(P)

Try adding the option -F SLXFQ

[Sparks]

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.

[manojkumarbioinfo]

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.