Novoindex cant open .fa file

[polsum]

Hi there, I am a very beginner of bioinformatics. I am trying to index mouse chromosome 1 fasta file in my Mac by using novoindex, but i get an error message "error: cant open chr1.fa". is it because the file is too big (200 MB)?

thanks in advance

[What_Da_Seq]

Make sure you have the file in the same directory as the novoindex executable or if not you have to use the proper path to the file. Hope that helps. I am indexing 3GB .fa files so it should not be a size issue.

[polsum]

Make sure you have the file in the same directory as the novoindex executable or if not you have to use the proper path to the file. Hope that helps. I am indexing 3GB .fa files so it should not be a size issue.

Thanks for the reply. I started using Bowtie now and it works just fine eventhough there are small issues.