Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Paired-end Illumina RNA-seq adapter trimming

    Does anyone can recommend a tool for Paired-end Illumina RNA-seq adapter trimming? Most of tools are for single-end sequence. I think if there a tools used for paired-end data.
    The shortcoming of the single end tools:
    1, The single end tools sometimes will make the paired-end data mess.
    2, It does not consider paired-end information, if there is a tool for paired-end, such remove will be accurately.

  • #2
    HTSeq has facilities useful for this.

    You can write a little Python script like this:

    Code:
    import itertools
    import HTSeq
    
    in1 = iter( HTSeq.FastqReader( "mydata_1.fastq" ) )
    in2 = iter( HTSeq.FastqReader( "mydata_2.fastq" ) )
    out1 = open( "trimmed_1.fastq", "w" )
    out2 = open( "trimmed_2.fastq", "w" )
    
    for read1, read2 in itertools.izip( in1, in2 ):
       read1.trim_right_end( "ACGGTC" )
       read2.trim_left_end( "TTCGAC" )
       read1.write_to_fastq_file( out1 )
       read2.write_to_fastq_file( out2 )
          
    out1.close()
    out2.close()
    I haven't tested the script, and you will have to adjust it to your needs, of course.

    Note that you can make the trimming tolerant to read errors by either adding a second argument, giving the allowed fraction of mismatches, or using trim_right_end_with_quals, which accepts a maximum sum of mismatch qualities. See here and here for an explanation.

    Comment


    • #3
      Simon Anders,
      Thanks for your reply.
      Could you please also give an example how to trim 3' reads which have low quality? For example, set a cutoff value. Bellow this cutoff, the nucleotide will be trimmed.

      Thanks.

      Comment


      • #4
        Take a look at "http://solexaqa.sourceforge.net/". It works on both single and paired-end reads.

        Comment


        • #5
          We have the same problem for paired-end of 100bp and sizing of 200 (fragment size) from Illumina GAIIx RNAseq. In many case we think we got an adapter in 3' that have been sequenced... we think that because the mapping is very bad in 3'. BUT we know that the Quality score is very good (Q> 30). The problem is the 3'end can contains just some bases from the adapter and not the complete sequence... when the list of adapter is known did you find a tool to solve this problem ?

          Thanks, vb

          Comment


          • #6
            Trimmomatic

            We are using Trimmomatic as it is able to do trimming and adaptor removal for paired-end reads. At first we tried fastx-toolkit but then we switched to trimmomatic as a better choice for paied-end samples.

            Comment


            • #7
              skewer

              You may also try skewer which is an adapter trimmer dedicated to Illumina paired-end data
              Last edited by relipmoc; 09-23-2013, 05:23 PM. Reason: title

              Comment


              • #8
                May i know from where to download skewer ?

                Comment


                • #9
                  Hi saran.ela123

                  you can download it from here: http://sourceforge.net/projects/skewer/files/

                  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
                  10 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, Yesterday, 06:07 PM
                  0 responses
                  9 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