Tophat2 Error With Repeat-Masked Genome!!

Question

[Rahul Sharma]

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

[Devon Ryan]

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

[Rahul Sharma]

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.