Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Struggling with quality trimming

    Hello everybody,

    this is my first try to trim Illumina (paired-end) reads on the unix command line.
    If i get it correctly, de-multiplexing was already done by the sequencing service.
    I guess this also means that the adapters are also gone already.

    What i want to do is trimming the reads by quality.
    I checked it on FastQC and want to get rid of read with a quality below 20.

    I tried trim_galore with
    trim_galore ../name1.fastq -q 20 --paired > trim_name.fastq

    which gives me:
    "No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)
    Please provide an even number of input files for paired-end FastQ trimming! Aborting ..." <- i got the idea of this line

    But i don't really know how to find out how my data are encoded.
    The data look like this.

    @NS500339:99:H3H52AFXX:1:11101:5599:1027 2:N:0:GTGAAA
    NNNCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGANANCTCNNAAAA
    +
    ###/AEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEE<6/<EEEEEEEEAAE6EEE/EEEEEEEEEEEAAEEEEE/6EE<AEEEEAEA<EEE/EEE/AAAE#<#<A/##/<<6


    I also tried fastx toolbox with the following command
    fastq_quality_filter -q 20 -i ../name.fastq -v -o trimmed_name.fastq

    The program works,
    Minimum percentage: 0
    Input: 4564772 reads.
    Output: 4564772 reads.
    discarded 0 (0%) low-quality reads.

    but if i check it again with FastQC, there are still reads with a quality below 20.


    Maybe someone can please help me with one of the programs.

    Thanks a lot, Alex

  • #2
    Grab a copy of BBMap and then run

    Code:
    $ zcat yourfile.fastq.gz | head -20 > new.fq
    $ testformat.sh in=new.fq
    to identify the format of the encoding in your file.

    While you have a copy of BBMap handy, use bbduk.sh to do trimming.

    Code:
    $ bbduk.sh -Xmx1g in=reads.fq.gz out=clean.fq.gz qtrim=r trimq=10

    Comment


    • #3
      Thanks

      Thanks a lot, if now the following mapping step also works, this will be the solution

      Comment


      • #4
        You could stay with BBMap and use bbmap.sh to do the mapping as well.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM
        • seqadmin
          Multiomics Techniques Advancing Disease Research
          by seqadmin


          New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

          A major leap in the field has
          ...
          02-08-2024, 06:33 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 06:12 AM
        0 responses
        13 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-23-2024, 04:11 PM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2024, 08:52 AM
        0 responses
        70 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-20-2024, 08:57 AM
        0 responses
        61 views
        0 likes
        Last Post seqadmin  
        Working...
        X