Question: Tophat failed at 'Mapping left_kept_reads to transcriptome'
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gravatar for biocyberman
4.4 years ago by
biocyberman800
Denmark
biocyberman800 wrote:

I am trying to run tophat for color-space data. The error is not very helpful for me to know what's wrong.

Any help is much appreciated. 

        tophat2 -p 14 -G $gtf --bowtie1 --color --zpacker pigz -o ${f}_tophat \
        --rg-id $f --rg-sample $f --rg-platform 'SOLiD.Wildfire' \
        --rg-library $f --rg-description 'Merged data from three lanes' \
        $bowtieIDX  trimmed_joined.${f}.fastq.gz

 

 

[2015-06-11 12:25:27] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-06-11 12:25:27] Checking for Bowtie
                  Bowtie version:        1.1.1.0
[2015-06-11 12:25:27] Checking for Bowtie index files (genome)..
[2015-06-11 12:25:27] Checking for reference FASTA file
[2015-06-11 12:25:27] Generating SAM header for /data/rn6/bowtie/rn6.color
[2015-06-11 12:25:35] Reading known junctions from GTF file
[2015-06-11 12:25:42] Preparing reads
         left reads: min. length=25, max. length=75, 106304325 kept reads (105371 discarded)
[2015-06-11 12:44:25] Building transcriptome data files LT1_tophat/tmp/Rattus_norvegicus.Rnor_6.0.80.chrFixed.ercc
[2015-06-11 12:44:39] Building Bowtie index from Rattus_norvegicus.Rnor_6.0.80.chrFixed.ercc.fa
[2015-06-11 12:48:27] Mapping left_kept_reads to transcriptome Rattus_norvegicus.Rnor_6.0.80.chrFixed.ercc with Bowtie
        [FAILED]
Error running bowtie:
Too few quality values for read: 3T3@
        are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'

 

rna-seq tophat • 2.4k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by biocyberman800
1

It looks like your fastq file is corrupt or otherwise malformed.
 

ADD REPLYlink written 4.4 years ago by Devon Ryan92k
Yes, I also had a hunch on this. BUT it is not my original fastq.gz file. It has something to do with `--zpacker` param and `--unmapped-fifo` param. I am not sure what to put for `--unmapped-fifo`.
ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by biocyberman800

Those are obscure enough parameters that I don't think I've ever seen anyone change them. Try using the defaults first to see if that at least runs.

ADD REPLYlink written 4.4 years ago by Devon Ryan92k

see Tophat Fails At Mapping Right_Kept_Reads To Genome With Bowtie

ADD REPLYlink written 4.4 years ago by Martombo2.5k
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