Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RNA seq data preprocessing and cleaning

    Hi All,

    I am a total newbies in this field. I have to assemble RNA seq data. Before that I need to trim the sequences. I have got 100bp illumina paired end reads in two files. I also got the adaptors sequences P5 and P7.
    5-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC-(insert)-ACCTTAAGAGCCCACGGTTCCTTGAGGTCAGTGXXXXXXTAGAGCATACGGCAGAAGACGAAC-3
    I tried trim_galore... but still I can see these much of overrepresented sequences in the fastqc report.

    ATGACACTCAAACAGGCATGCTCCACGGAATACCATGGAGCGCAAGGTGC 1155666 2.5956349017221085 No Hit
    AATGACGCTCGAACAGGCATGCCCCTCGGAATACCAAGGGGCGCAATGTG 225179 0.5057538004361837 No Hit
    AAGACACTCAAACAGGCATGCCTCTCGGAATACCAAGAGGCGCAAGGTGC 218636 0.4910581711090531 No Hit
    GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA 119619 0.2686652123616139 Illumina RNA PCR Primer (100% over 50bp)
    GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA 111925 0.251384428005364 Illumina RNA PCR Primer (100% over 50bp)
    AAATGACGCTCAAACAGGCATGCCCTTTGGAATACCAAAGGGCGCAATGT 104210 0.2340564774843778 No Hit
    ACAAACCCTTGTGTCGAGGGCTGACTTTCAATAGATCGCAGCGAGGGAGC 71881 0.16144528987673504 No Hit
    GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAA 46463 0.10435626248303084 Illumina RNA PCR Primer (100% over 50bp)

    I wanted to know how i can remove this overrepresented sequences from my data and do i need to remove it all ?

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-27-2024, 06:37 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X