Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RNA-seq Quality Control help

    I am going to see the quality of the RNA-seq data, is any method or program available to help me to do this? Thanks!

    I heard some people analyze the distribution of ATCG in the different position of the reads... or compare the lane's complexity...

  • #2
    ShortRead could assess the data quality; and other stuffs could be used? How to evaluate the ribosomal RNA contaminations.... Thanks!

    Comment


    • #3
      I often use fastQC for this task.

      Comment


      • #4
        But I am not sure if fastQC can help with the ribosomal RNA contaminations.... I think there are some discussions about that in this forum.

        Comment


        • #5
          I will start from FastQC; any more packages for QC control? Thanks a lot!

          Comment


          • #6
            interpreting the QC

            Thanks again for your help!
            My samples were done in Illumina and I have used FastQC to check the quality of my samples, I have some questions as for 1) per sequence quality scores; 2)Sequence Duplication Levels;

            Q1: there are up-down peaks starting from position 1 to position 15, and my sequence length is 75nt; is this OK? I heard people said before 16 there are always some nosies....

            Q2: Sequence duplication levels and Kmer Content? first one is big than 69 and second one has some problems with the beginning sequences; is this also related to Q1


            I really appreciate all the helps from this forum, thanks a lot!


            Originally posted by ttnguyen View Post
            Last edited by lewewoo; 04-29-2011, 12:32 PM.

            Comment


            • #7
              Regarding rRNA contamination-
              I am not sure whether there is a database for ribosomal RNA like other RNA species(miRNA and ncRNA). If available, data can be blast against this database to see the contamination.

              Comment


              • #8
                EVER-seq (Evaluate Experiment of RNA-seq)

                Originally posted by ttnguyen View Post
                fastqc only check the quality of sequence per se (such as GC content, base calling quality, over represented kmer, etc), that's fundamental and important. However, fastqc does not tell you if the RNA-seq experiment was successful or not (it only tells you whether the sequencing was successful).

                We develop a package to QC RNA-seq experiment from different aspects such as: gene body coverage, reads distribution over the genome, duplication rate, reproducibility and saturation etc.



                We change the name of EVER-seq into RSeQC. Because Google Code doesn't allow rename an exist project, we create a new project with the url:


                From now on, we will update and add new modules to RSeQC
                Last edited by liguow; 02-21-2012, 09:48 AM.

                Comment


                • #9
                  The picard tool set also has a nice RNAseq metrics tool

                  Comment


                  • #10
                    You could also use the perl script preprocessest.pl with the -dr option set for the removal of ribosomal cDNA. You'd need to set up a blast db with your organism's rDNA first though.
                    Last edited by lukas1848; 11-02-2011, 03:32 AM.

                    Comment

                    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, Yesterday, 06:37 PM
                    0 responses
                    11 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, Yesterday, 06:07 PM
                    0 responses
                    10 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-22-2024, 10:03 AM
                    0 responses
                    51 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-21-2024, 07:32 AM
                    0 responses
                    67 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X