I have tried converting using the FASTX-toolkit in ubuntu but it is showing "Invalid quality score value (char ',' ord 44 quality value -20) on line 4". Even I tried with "reformat.sh" but throwing error on the terminal.
So can anyone suggest any other way to convert or any corrections needed in the command line?
There are many tools available for that. But I wonder are you just trying to directly convert Fastq to Fasta or during/with any analyses? Quality scores are present in sequence file for a purpose.
sir, Abhijeet Singh I was trying to convert the file during NGS analysis. I had done filtering and quality enhancement (quality control analysis) of the FASTq file. but for the further process, I needed that in the FASTA format.
During the process of adapter trimming, tools like cutadapt or trimmomatic can output fasta files direclty. There is no need to use any other tool for the purpose.
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