Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • FASTQ to FASTQSanger using Groomer question

    My data (paired end reads) come from Illumina Hiseq 2000 using multiplexed sequencing technology on Genome DNA seq. L6_R1 and L6_R2 is the pair from Lane 10. My data are as follows:

    File L6-R1
    @HWI-ST261:6:1:1385:2207#TAGCTT/1
    GGTTCGCATTAC...............ATTCATTCCCTGAT..................TTAAACT.................TTGTCCTTCTCAACTTG
    +
    ____`_```_W\BBBBBBBBBBBBBBBT\]\^^^^___`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

    File L6_R2

    @HWI-ST261:6:1:1663:2218#TAGCTT/2
    TGAG.AAT....TTTCGGGTT.....AGTTTT.......TCTCTGGGATTAGGGTTTACGAGTACGTGGATAATGGG.......................
    +
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB


    I used FASTQ Groomer on data L6_R1 and L6_R2. I chose Illumina 1.3 + as the input quality scores type and I got the report as follows
    Info: Groomed 118063852 illumina reads into sanger reads.
    Based upon quality and sequence, the input data is valid for: None
    Input ASCII range: 'B'(66) - 'h'(104)
    Input decimal range: 2 - 40

    Is it right for me to choose Illumina 1.3 + as Fastq data format?

  • #2
    Do you know what version of illumina pipeline was used to generate this data? If you do not know, it would be helpful to ask the folks who generated this data.

    Comment


    • #3
      That does look like Illumina 1.3 1.3 starts at ASCII 64, so @ is 0, and B is 2, which is really the lowest score, which is what you have there.

      So that much you did correctly, but it looks like your data is very poor quality, maybe that's why its being rejected.

      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, Today, 07:23 AM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-17-2024, 06:54 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-14-2024, 07:24 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-13-2024, 08:58 AM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Working...
      X