Bowtie Index building for wheat genome
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?
• 2,493 views
•
link
updated
by
Jeffin Rockey
•
written
by
K S •
•
written
by
K S •
1 answer
Install bowtie2 and use bowtie2-build to build index. It will automatically build .bt2l indices for wheat.
• 0 views
•
link
written
by
Jeffin Rockey
Are you sure the bowtie2-build completed successfully prior to attempting align? *2.bt2l seems to be of 0 size.
• 0 views
•
link
written
by
Jeffin Rockey
Try bowtie2-inspect wheat.fasta.bowtie > my_bowtie.fa
and compare the output to your wheat.fasta file.
• 0 views
•
link
written
by
michael.ante
Log in to answer this question.
More posts like this
-
samtools mpileup taking too long
written by K •
-
Plant small RNA (sRNA) data analysis pipeline
written by K S •
-
Reference genome of wheat for Bowtie
written by K S •
-
TOPHAT error in mapping left_kept_reads step during a mapping with fusion search with bowtie1
written by Gabriel Wajnberg
-
Tophat err =1
written by Harumi •
-
Mapping onto the Transcriptome, RNA-seq
written by asyndeton17 •
-
problem with tRNAseq alignment
written by alirezamomeni707 •
-
Am I using Tophat2 correctly? Segment-based junction search error keeps coming up.
written by aswartz85 •
-
Indexing a reference genome
written by maxgen •
-
How To Combine Multiple Indexed Files
written by fanx •
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).