Hi, all. I am new to informatics.
I have indexed human references sequences (chr1.fa, chr2.fa, etc) separately successfully using Bowtie 0.11.3. After that, I combine the 24 fa files into a large fa file chr.fa (2.9G). And then tried to index it. But I got this error: "Error: could not open + [my fa file path]"
The path is definitely correct. I have changed the mod of the file chr.fa to 777. Even I combined chrX.fa and chrY.fa to test.fa. This test.fa could be indexed! What is wrong with it?
The reference sequence file is 2.9G. I am using Fedora 11 with 4G memory. Is it the problem of memory? Or is there any built index provided by Bowtie?
By the way, I use bowtie 0.9 to index the human reference genome (24 chromosomes separately). The original size is 2.9G, and the indexed size is 3.0G, the memory footprint is 6.79G! Why is it like that? The number is far from the claimed value on official site. Did I do anything wrong? I used default setting of bowtie.
Thanks a lot.
I have indexed human references sequences (chr1.fa, chr2.fa, etc) separately successfully using Bowtie 0.11.3. After that, I combine the 24 fa files into a large fa file chr.fa (2.9G). And then tried to index it. But I got this error: "Error: could not open + [my fa file path]"
The path is definitely correct. I have changed the mod of the file chr.fa to 777. Even I combined chrX.fa and chrY.fa to test.fa. This test.fa could be indexed! What is wrong with it?
The reference sequence file is 2.9G. I am using Fedora 11 with 4G memory. Is it the problem of memory? Or is there any built index provided by Bowtie?
By the way, I use bowtie 0.9 to index the human reference genome (24 chromosomes separately). The original size is 2.9G, and the indexed size is 3.0G, the memory footprint is 6.79G! Why is it like that? The number is far from the claimed value on official site. Did I do anything wrong? I used default setting of bowtie.
Thanks a lot.
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