Bowtie Index building for wheat genome

Question

[K S]

I am trying to build the index file for mapping my small RNA sequencing onto the wheat genome (~15 GB). I am bowtie-build

bowtie-build wheat.fasta wheat.fasta.bowtie

However, I am receiving an error that the file is too long. Is there any way to prepare the index using one single file?

[michael.ante]

Hi,

the wheat genome may be too big due to its chromosomes' length exceeding the size allocated for storing it, see e.g. The Longest Chromosome > Sizeof(Int32). You can generate a STAR index, but you'll need a lot of RAM (>= 126GB).

Answer 1

[Jeffin Rockey]

Install bowtie2 and use bowtie2-build to build index. It will automatically build .bt2l indices for wheat.

[K S]

Thank you. Four files have been generated using

bowtie2-build wheat.fasta wheat.fasta.bowtie

*1.bt2l (16 Mb) *2.bt2l (0) *3.bt2l (12M) *4.bt2l (3.4G)

However, I am receiving an error message (ERR): bowtie2-align exited with value 1

[Jeffin Rockey]

Are you sure the bowtie2-build completed successfully prior to attempting align? *2.bt2l seems to be of 0 size.

[michael.ante]

Try bowtie2-inspect wheat.fasta.bowtie > my_bowtie.fa and compare the output to your wheat.fasta file.