I'm working with my first Illumina sequence reads and using Bowtie for alignment to the reference genome. I must be doing something wrong, because the SAM files that are generated are over 50 GB in size. It seems to be some sort of loop, because the algorithm is halted once my disk quota is exceeded.
The Illumina read files are about 4 GB after conversion to FASTQ Sanger format.
I've posted the script below for anyone who can tell me where I'm messing up:
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#BSUB -J BowtieSwineSeq4
#BSUB -o BowtieSwineSeq4.o%J
#BSUB -e BowtieSwineSeq4.e%J
#BSUB -n 2
bowtie -p 2 -a -v 2 -t -S SwineGenome9.58 s_4_sequence.fastq SwineSeq4.sam
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Many thanks in advance,
JJW
The Illumina read files are about 4 GB after conversion to FASTQ Sanger format.
I've posted the script below for anyone who can tell me where I'm messing up:
-----
#BSUB -J BowtieSwineSeq4
#BSUB -o BowtieSwineSeq4.o%J
#BSUB -e BowtieSwineSeq4.e%J
#BSUB -n 2
bowtie -p 2 -a -v 2 -t -S SwineGenome9.58 s_4_sequence.fastq SwineSeq4.sam
-----
Many thanks in advance,
JJW
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