Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Saeideh
    replied
    Alriiiiiight...

    I got it

    Thanks all

    Leave a comment:


  • yueluo
    replied
    That is not a valid fasta file.

    https://en.wikipedia.org/wiki/FASTA_format

    Leave a comment:


  • Saeideh
    replied
    I put following sequences in Over.fasta

    CTCCCATTTCGCTCGCCGCTACTACGGGAATCGCTTTTGCTTTCTTTTCC
    GGCTTGCGGTGGATACCTAGGTACCCAGAGACGAGGAAGGGCGTAGCAAG

    Isn't it correct?

    Leave a comment:


  • kmcarr
    replied
    Originally posted by Saeideh View Post
    ILLUMINACLIP: Using 0 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
    The explanation is here (highlighted in red). Trimmomatic is not finding any valid sequences to use for trimming in the supplied clipping file 'Over.fasta' meaning you must have formatted it incorrectly.

    Leave a comment:


  • Saeideh
    replied
    Yes, I'm almost sure because when I do fastqc, the number of reads and nucleotides in them have not changed (I mean "Total sequences" and "Sequence length").

    Leave a comment:


  • yueluo
    replied
    Are you sure nothing was done the your sequences? 100% reads surviving does not necessarily mean no trimming was performed, especially when you don't specify MINLEN.

    Leave a comment:


  • Saeideh
    started a topic Trimmomatic but no trimming

    Trimmomatic but no trimming

    Hii dear friends

    I have a question about Trimmomatic. I wrote this command:

    java -jar /usr/bin/trimmomatic-0.33.jar PE -phred64 72_L3_1.fq.gz 72_L3_2.fq.gz 71P_1.fq.gz 71UP_1.fq.gz 71P_2.fq.gz 71UP_2.fq.gz ILLUMINACLIP:Over.fasta:2:40:15


    72_L3_1.fq.gz
    and
    72_L3_2.fq.gz
    are my input files

    71P_1.fq.gz
    71UP_1.fq.gz
    71P_2.fq.gz
    and
    71UP_2.fq.gz
    are my output files. In my case P means paired and UP means unpaired.

    after I did fastqc I got overrepresented sequence (it is not adapter) and I stored it in Over.fasta and I want to trim it from my data.

    but when I run the command I see this:

    ILLUMINACLIP: Using 0 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
    Input Read Pairs: 19759652 Both Surviving: 19759652 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)

    It does not trim the sequence.

    Why it is like that?

    In addition, for Palindrome and Single mode U just selected 40 and 15 because the manual selected them. Actually I do not know which score I should select. How can I choose the correct score?

    Would you please help me in these two questions.

    -------------------------------------------------------------------
    I'm sorry for asking so many questions each day. I' working with RNA-seq data in these days. In each level, I should stop due to errors, warnings, blocks and confusions and this story continues.

    and thank you for helping me in solving all these problems.

Latest Articles

Collapse

  • seqadmin
    Choosing Between NGS and qPCR
    by seqadmin



    Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
    10-18-2024, 07:11 AM
  • seqadmin
    Non-Coding RNA Research and Technologies
    by seqadmin




    Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

    Nobel Prize for MicroRNA Discovery
    This week,...
    10-07-2024, 08:07 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 11-01-2024, 06:09 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-30-2024, 05:31 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-24-2024, 06:58 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-23-2024, 08:43 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Working...
X