Hello! I am currently facing a challenge of filtering out low quality sequences (output from Sanger sequecing, roughly I have 300 sequences, command line are very much appreciated).
Below, I explain what I have done so far, and I am looking for any hints/tips to get this working.
1- conversion ab1 to fastq " for filename in *.ab1; do seqret $filename fastq_files/$filename.fastq -osformat fastq; done"
2- trimming sequencing "for filename in *.fastq; do fastx_trimmer -f 30 -l 600 -i $filename -o t_$filename ; done"
3- trying to filter the sequences using " quality fastq_quality_filter -i input.fastq -o output/output.fastq -q 20 -v -Q 33 " and I got the following error message,
stack smashing detected : fastq_quality_filter terminated zsh: abort (core dumped) fastq_quality_filter -i PosKonR.fastq -o output/Pos.fastq -q 20 -v -Q 33
I changed to -Q 64 and got " fastq_quality_filter: Invalid quality score value (char '&' ord 38 quality value -26) on line 4 "
Many thanks in advance for any help on this