Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How good bowtie can map SOLiD data?

    I tried the following command to map the attached fq file (single end, ChIP-seq).

    bowtie -C -p $threads -n 3 -e 160 -a -m 1 --best --strata $BOWTIE2_INDEX/hg19_c s_6.fq -S s_6n.sam 2>&1 | tee s_6n.log

    The mappable reads are of only 35%.

    # reads processed: 2500
    # reads with at least one reported alignment: 885 (35.40%)
    # reads that failed to align: 1376 (55.04%)
    # reads with alignments suppressed due to -m: 239 (9.56%)
    Reported 885 alignments to 1 output stream(s)

    The following command gives 38% (as -e is large)

    bowtie -p 8 -C -m 10 -l 27 -n 3 -e 950 -k 1 $BOWTIE_INDEX/hg19_c s_6.fq -S s_6.sam 2>&1 | tee s_6.log
    # reads processed: 2500
    # reads with at least one reported alignment: 972 (38.88%)
    # reads that failed to align: 1275 (51.00%)
    # reads with alignments suppressed due to -m: 253 (10.12%)
    Reported 972 alignments to 1 output stream(s)

    But supposedly, SOLiD pipeline should be able map this file for over 50%. Does anybody know how good bowtie is to map SOLiD files? Are there any other parameters that can improve the results?

    I see that people said, bfast is better than bowtie for default parameters. By tuning the parameter, can the results of bowtie be improved? Thanks!

    http://seqanswers.com/forums/showpos...28&postcount=3
    Attached Files

  • #2
    We've mapped SOLiD RNAseq data with several mappers (Bowtie, BWA, bfast) and never got above 25-35% mapped. Others we have spoken to are getting similar results (or worse).

    Would be curious to know if anyone has mapped better.

    Comment


    • #3
      we mapped SOLiD with low mapped rate too!

      we mapped SOLiD with low mapped rate too!
      I used tophat to analyse it ! They are colorspace pair end reads.
      Originally posted by Jean View Post
      We've mapped SOLiD RNAseq data with several mappers (Bowtie, BWA, bfast) and never got above 25-35% mapped. Others we have spoken to are getting similar results (or worse).

      Would be curious to know if anyone has mapped better.

      Comment


      • #4
        I have mapped 70-80% with BioScope for some SOLiD RNA-seq data (paired or not). But in many cases also much less. With Bowtie maybe 50% in the best cases.

        Comment


        • #5
          I was talking to someone the other day who said they got >50% mapping with Novoalign. If I recall correctly. Actually they seemed to read SeqAnswers, so maybe they would chime in?

          --
          Phillip

          Comment


          • #6
            I have 3 RNA-seq libraries generated on Solid5500. 64%-72% of the reads mapped with Lifescope.

            Comment


            • #7
              I got best results with -v1 -m1 with bowtie on colorspace.

              run bowtie then bfast on colorspace reads. Contribute to brentp/bowfast development by creating an account on GitHub.

              Comment


              • #8
                We've been getting 30-50% mapping for SOLiD4 reads using Bowtie. It has been as low as ~9% for a very low-read sample (~400k reads multiplexed in with other samples totalling ~400M reads).

                Comment


                • #9
                  Based on my mapping results,the same RNA-seq sample mapped by tophat and lifescope got ~50% and ~80% mappable reads, respectively, even we have used the additional ECC primer.

                  I guess the Refcor module in lifescope may improve the mappable rate.
                  Yi John Huang (PhD student)
                  886-3-2118800 ext. 3731
                  Graduate Institute of Biomedical Science, Chang Gung University

                  Comment


                  • #10
                    sure, the process used by Lifescope (which includes end clipping) increases the mappable reads. That doesn't necessarily mean it's a better result -- I can increase the sensitivity of a clinical test to 100% by always reporting a positive result.

                    Comment


                    • #11
                      For human exome reads we generally get the following figures:

                      Bowtie ~35%
                      BWA 0.5.x ~40%
                      Clcbio ~50-60%
                      NovoalignCS ~55-65% *
                      Lifescope ~70-80% *



                      *use end clipping.
                      Iteratively trimmed reads are still very useful, provided you don't make them too short.

                      Bowtie1 is not that useful for long reads, as it only allows max 3 mismatches in the seed. Apparently more mismatches are necessary for useful mapping of Solid data as said by someone about using bwa successfully.

                      As discussed here before, % alignments isn't really the best quality criterion for an aligner. We prefer NovoalignCS to date based on clean alignments and SNPs called versus the others via a standard pipeline.

                      Comment


                      • #12
                        So sad! I have been tweaking the parameters on Bowtie to get some huge runs to map decently, but so far the max I've gotten is 3% using -l 17 -n 3 !!!! Do you think it might be better to use -v ?

                        Seeded quality full-index search: 16:45:26
                        # reads processed: 60132812
                        # reads with at least one reported alignment: 1882083 (3.13%)
                        # reads that failed to align: 58250729 (96.87%)
                        Reported 4232170 paired-end alignments to 1 output stream(s)
                        Time searching: 16:45:30
                        Overall time: 16:45:30

                        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