Question: Tophat2 Error With Repeat-Masked Genome!!
gravatar for Rahul Sharma
6.5 years ago by
Rahul Sharma600
Rahul Sharma600 wrote:

Dear all,

I was trying to map the RNA seq data on the assembled genome. I was using Tophat tophat-2.0.10.Linux_x86_64 and Bowtie2 bowtie2-2.1.0. When I tried to input the index of repeat masked genome (Masking was done by RepeatModeler; Genome size 78Mb; Repeats: 42%). Tophat2 is giving me following error message:

bowtie2-inspect SCa_gtr_500_discarded_90_percent_Ns_ID_renamed.fasta.masked.indexassert_eq: expected (1816, 0x718) got (1536, 0x600) bt2_inspect.cpp:218 bowtie2-inspect: bt2_inspect.cpp:218: void print_ref_sequences(std::ostream&, bool, const EList<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, 128>&, const uint32_t*, const std::string&): Assertion 0' failed. Aborted

But when I did the same thing on the unmasked genome, it is running fine now. My questions are,

a). Is this error is usual with all repeat-masked genomes?

b). I need to predict genes using Reference based RNA-Seq assembly, so should I really do reads mapping on the repeat-masked genome?

c). I am interested in finding genes on the repeat-masked genome, how can we fix this problem?

I would really appreciate your comments on this!

Best regards, Rahul

bowtie2 tophat2 • 2.1k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Rahul Sharma600

Is the result of repeat masking that there are some contigs with only Ns? If you

ADD REPLYlink written 6.5 years ago by Devon Ryan95k

Yes, I filtered out those scaffolds which were having only Ns. Now it is running fine. But Bowtie2 should also print it as an error message.

ADD REPLYlink written 6.5 years ago by Rahul Sharma600
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