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  • Tophat Does not Work with SOLiD Reads

    I have been trying for several weeks to run Tophat on SOLiD reads but I got the same error message every time. While I searched a lot of forums and related questions but could not find a solution.

    a sample of my data is:
    =====
    @SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
    T02213232.20202212300333
    +SRR179591.60.1 mendel_20110320_FRAG_BC_Ryan_RNA_Seq_2_70_490_F3 length=50
    !<=B?@=7B!8>;@BB<:@-<259
    =====

    I use Tophat v2.0.13 and the error message that I got is:
    =====
    [2015-01-22 11:01:43] Beginning TopHat run (v2.0.13)
    -----------------------------------------------
    [2015-01-22 11:01:43] Checking for Bowtie
    Bowtie version: 1.1.1.0
    [2015-01-22 11:01:43] Checking for Bowtie index files (genome)..
    [2015-01-22 11:01:43] Checking for reference FASTA file
    [2015-01-22 11:01:43] Generating SAM header for HumanGenome/Ensemble78/HumanIndexedGenome/Bowtie1ColorSpace//Human
    Warning: found a read < 20bp in SRR179592_Trimmed.fastq
    [2015-01-22 11:02:06] Reading known junctions from GTF file
    [2015-01-22 11:02:55] Preparing reads
    left reads: min. length=19, max. length=50, 20533939 kept reads (147 discarded)
    Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped in too many places
    [2015-01-22 11:08:48] Building transcriptome data files TophatAlignment/tmp/Homo_sapiens.GRCh38.78
    [2015-01-22 11:10:07] Building Bowtie index from Homo_sapiens.GRCh38.78.fa
    [2015-01-22 11:44:10] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh38.78 with Bowtie
    [FAILED]
    Error running bowtie:
    Too few quality values for read: 1T0B
    are you sure this is a FASTQ-int file?
    terminate called after throwing an instance of 'int'
    ========

    The command that I used to run Tophat is:
    =====
    tophat --color --bowtie1 -o out -r 500 --mate-std-dev 500 --no-mixed -p 16 -G Homo_sapiens.GRCh38.78.gtf Bowtie1ColorSpace/Human Reads_Trimmed.fastq
    =====
    Last edited by Fernas; 01-30-2015, 03:46 AM.

  • #2
    Re: Tophat Does not Work with SOLiD Reads

    I have same problem.
    I added following option as shown in Tophat manual (http://ccb.jhu.edu/software/tophat/manual.shtml)
    --library-type secondstrand

    This option doesn't work as well.
    Last edited by jcjeong; 06-09-2015, 10:21 AM.

    Comment


    • #3
      I have the same problem. Were you ever able to find a solution?

      Comment


      • #4
        AFAIK, only Tophat version 1 is capable of aligning colorspace reads.
        You need to download and run a much older version than (v2.0.13) from http://ccb.jhu.edu/software/tophat/downloads/

        Comment


        • #5
          Originally posted by Michael.Ante View Post
          AFAIK, only Tophat version 1 is capable of aligning colorspace reads.
          You need to download and run a much older version than (v2.0.13) from http://ccb.jhu.edu/software/tophat/downloads/
          I know this is an old post but in case anyone need it I will post.
          You can use TopHat2 but with --bowtie1 parameter. This will use bowtie1 to map the color reads (bowtie2 is not able to do it), so there is no need to download an old TopHat version.

          Comment

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