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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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Issue with fastq after converting phred 64 to phred 33 quality scores #118

Open kgaonkar6 opened 6 years ago

kgaonkar6 commented 6 years ago

Hello,

I ran seqtk seq -VQ64 read1.fastq.gz > read1_phred33.fastq to convert my 64 based phred score reads to 33 based phred score phred reads. However when I attempted to run them through tophat alignment I got this error:

Saw ASCII character 4 but expected 33-based Phred qual. terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

Since the conversion is generating lower ASCII values than allowed for 33-based Phred quality score How do I go about fixing this issue with the fastqs?

peterjc commented 5 years ago

Can you share a few reads from your file which show this problem? i.e. Identify the read with the ASCII character 4 in it, and show it here before and after running seqtk seq