Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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/

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Best Practices for Single-Cell Sequencing Analysis
      by seqadmin



      While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
      06-06-2024, 07:15 AM
    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      05-24-2024, 01:16 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 07:49 AM
    0 responses
    14 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-20-2024, 07:23 AM
    0 responses
    14 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-17-2024, 06:54 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 06-14-2024, 07:24 AM
    0 responses
    25 views
    0 likes
    Last Post seqadmin  
    Working...
    X