Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • skbrimer
    Member
    • Mar 2014
    • 55
    #1

    Split N Trim RNAseq data

    Hello everyone,

    I have more of a general pre-processing question. We are doing some small viral genome sequencing. The virus is ssRNA (coronaviridae) and we have been using the RNAseq method on the PGM and I was just wondering if I'm doing the pre-processing correctly.

    I have been treating the reads like genomic DNA for the processing, which is just mapping to the reference and marking duplicates. Is this correct? Should I be looking for splits? I know that viruses have different splices to make early and late proteins, but not really these two genes make one protein splices.

    The more I thought about it the more unsure I became, does anyone have an opinion?
    Tags: None
  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709
    #2
    It seems prudent to map with a splice-aware aligner, just to be on the safe side.

    Comment

    • SylvainL
      Senior Member
      • Feb 2012
      • 180
      #3
      Hi,

      simply tell us with mapper you used. If you used bowtie2 it should be fine...

      Comment

      • skbrimer
        Member
        • Mar 2014
        • 55
        #4
        Hi everyone! Thank you for the input, I am using TMAP(modified BWA) and BWA. So I have not used bowtie 2 before but it is a splice aware mapper correct? So I have 2 votes for using a splice aware vs a non-splice aware. Correct?

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142
          #5
          Add BBMap to the list if you are looking at alternates.

          Comment

          • Brian Bushnell
            Super Moderator
            • Jan 2014
            • 2709
            #6
            Originally posted by skbrimer View Post
            Hi everyone! Thank you for the input, I am using TMAP(modified BWA) and BWA. So I have not used bowtie 2 before but it is a splice aware mapper correct? So I have 2 votes for using a splice aware vs a non-splice aware. Correct?
            No, Bowtie2 is not splice-aware.

            Originally posted by GenoMax View Post
            Add BBMap to the list if you are looking at alternates.
            +1

            Comment

            • SylvainL
              Senior Member
              • Feb 2012
              • 180
              #7
              Yep, actually my mistake. I wanted to mention STAR (based on Bowtie2) which is splice-aware...
              You can also use TopHat but, to my knowledge, bwa is not splice-aware...

              Comment

              • westerman
                Rick Westerman
                • Jun 2008
                • 1104
                #8
                Originally posted by SylvainL View Post
                ... You can also use TopHat but, to my knowledge, bwa is not splice-aware...
                What do those two sentence parts have to do with each other? Tophat is splice-aware and uses bowtie2 as its mapping engine.

                Comment

                • SylvainL
                  Senior Member
                  • Feb 2012
                  • 180
                  #9
                  skbrimer mentioned he used bwa, which is not splice aware. And I spoke about TopHat (and STAR in a previous answer) which are both splice-aware... I did not mean that TopHat was based on bwa...

                  Comment

                  Previous template Next

                  Latest Articles

                  Collapse
                  • SEQadmin2
                    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
                    by SEQadmin2


                    I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

                    Here are nine questions we think about, in roughly the order they matter, before...
                    06-18-2026, 07:11 AM
                  • SEQadmin2
                    From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
                    by SEQadmin2


                    Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

                    The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
                    ...
                    06-02-2026, 10:05 AM
                  • SEQadmin2
                    Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
                    by SEQadmin2


                    With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

                    Introduction

                    Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
                    05-22-2026, 06:42 AM
                  View All

                  ad_right_rmr

                  Collapse

                  News

                  Collapse
                  Topics Statistics Last Post
                  Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
                  Started by SEQadmin2, 06-17-2026, 06:09 AM
                  0 responses
                  21 views
                  0 reactions
                  		 Last Post SEQadmin2
                  by SEQadmin2
                  06-17-2026, 06:09 AM  
                  Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2
                  Started by SEQadmin2, 06-09-2026, 11:58 AM
                  0 responses
                  40 views
                  0 reactions
                  		 Last Post SEQadmin2
                  by SEQadmin2
                  06-09-2026, 11:58 AM  
                  A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2
                  Started by SEQadmin2, 06-05-2026, 10:09 AM
                  0 responses
                  46 views
                  0 reactions
                  		 Last Post SEQadmin2
                  by SEQadmin2
                  06-05-2026, 10:09 AM  
                  A New Single-Cell Method Maps DNA-Protein Interactions by SEQadmin2
                  Started by SEQadmin2, 06-04-2026, 08:59 AM
                  0 responses
                  49 views
                  0 reactions
                  		 Last Post SEQadmin2
                  by SEQadmin2
                  06-04-2026, 08:59 AM  
                  View All
                  Working...