Hello I'm trying to use Bowtie2-Build on the Pig Fastq SRR689228.fastq. I'm getting a error sayings its the file is too big.
How can I fix this problem?
How can I fix this problem?
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There are two problems here. First, you're trying to index the reads; you need to index the reference (the fasta file), not the fastq file.
Second, you might be using an old version of bowtie2; I believe current versions can handle genomes over size 2^32-1 bases. But, that's not really too important here as the pig genome is probably similar in size to human, or around 3Gbp. -
Have you tried the "bowtie-build --large-index" option?
Valid only if you are trying to build the index with the genome fasta file as Brian points out above.Comment
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Ok I will index the file and trying Bowtie 2 Large optionLast edited by Milestailsprowe; 08-12-2015, 08:45 AM.Comment
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At a minimumOriginally posted by Milestailsprowe View Post
I suggest that you save yourself some trouble and download the sequence/annotation/index bundle from: http://support.illumina.com/sequenci...e/igenome.htmlCode:$ bowtie2-build pig_genome.fa pig_genome
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