[Bio-Linux] tophat 2.0.13 missing reads

[Tim Booth]

Hi All,

I just wanted to report back to this list that there was, indeed, an
issue with Tophat 2.0.13 which was on Bio-Linux since December last
year.

See comments from @gpertea on
https://github.com/infphilo/tophat/issues/18

So if you have used Tophat for something this year you should consider
re-running the alignment with the new updated version to check your
results, even if you did not use multi-thread mode.

Best,

TIM

On Fri, 2015-08-21 at 13:48 -0400, Josh Thackray wrote:
> Hi All,
> 
> I am running tophat (version 2.0.13, from the biolinux distribution). I 
> am facing a problem where running tophat with increasing values for -p 
> (number of threads) results in more and more reads lost in the final 
> output. I'm starting with an uncompressed fastq file containing  
> 18,115,321 reads, and running tophat with default parameters except for 
> -p and -o.
> 
> Running -p 8 results with the following information in align_summary.txt:
>      Input     :    318640
>      Mapped:    191949 (60.2% of input)
>      of these:     29316 (15.3%) have multiple alignments (0 have >20)
>      60.2% overall read mapping rate.
> 
> Running -p 4 results with the following information in align_summary.txt:
>      Input     :   1302700
>      Mapped:     759998 (58.3% of input)
>      of these:     115861 (15.2%) have multiple alignments (1 have >20)
>      58.3% overall read mapping rate.
> 
> Running -p 1 results with the following information in align_summary.txt:
>      Input     :  18115321
>      Mapped:  12014534 (66.3% of input)
>      of these:   1867188 (15.5%) have multiple alignments (13 have >20)
>      66.3% overall read mapping rate.
> 
> I also tried running tophat with the --no-sort-bam option to check if 
> samtools was somehow screwing up during the mergesort operation, but I 
> get the same result. I also confirmed the numbers reported in the 
> align_summary.txt file using the samtools flagstat command. Further 
> using bowtie1 instead of bowtie2 for the alignment engine did not 
> resolve the problem of these reads going missing.
> 
> Any ideas???
> 
> Thanks,
> 
> Josh
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

Centre for Ecology and Hydrology
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