Hi all,
I am working on aligning a set of paired-end reads with bowtie. I am trying to generate my reference index using:
/data/apps/bowtie/./bowtie-build -r pombe_fasta/chromosome1.fasta,pombe_fasta/chromosome2.fasta,pombe_fasta/chromosome3.fasta pombe_indexes/
It generates pombe.1.ebwt, pombe.2.ebwt,pombe.1.rev.ebwt,pombe.2.rev.ebwt
When that failed to generate the files for paired-end alignment i tried the -3 option which also didn't generate the files.
I was wondering what I can do to generate the two files needed for paired-end alignments, or if anyone has pre-built indexs for Pombe.
I am utilizing:
/data/apps/bowtie/bowtie-build version 0.11.3
64-bit
Built on privet.umiacs.umd.edu
Mon Oct 12 18:08:44 EDT 2009
Compiler: gcc version 3.4.6 20060404 (Red Hat 3.4.6-10)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
I am working on aligning a set of paired-end reads with bowtie. I am trying to generate my reference index using:
/data/apps/bowtie/./bowtie-build -r pombe_fasta/chromosome1.fasta,pombe_fasta/chromosome2.fasta,pombe_fasta/chromosome3.fasta pombe_indexes/
It generates pombe.1.ebwt, pombe.2.ebwt,pombe.1.rev.ebwt,pombe.2.rev.ebwt
When that failed to generate the files for paired-end alignment i tried the -3 option which also didn't generate the files.
I was wondering what I can do to generate the two files needed for paired-end alignments, or if anyone has pre-built indexs for Pombe.
I am utilizing:
/data/apps/bowtie/bowtie-build version 0.11.3
64-bit
Built on privet.umiacs.umd.edu
Mon Oct 12 18:08:44 EDT 2009
Compiler: gcc version 3.4.6 20060404 (Red Hat 3.4.6-10)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
Comment