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  • filtering out low quality sequences from Sanger Sequencing

    Hello!
    I am currently facing a challenge of filtering out low quality sequences (output from Sanger sequecing, and roughly I have 300 sequences to process).

    Below, I explain what I have done so far, any hints/tips to get this working are very much appreciated.

    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 how overcome this issue.

  • #2
    Cross-posted: https://www.biostars.org/p/312889/

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