Hello I'm trying to align a bowtie2 index file with a fasta file. No matter what I do it ends with value of 1. How do I stop this?
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Originally posted by dpryan View PostTry building the index for "genome.fa" first:
Code:bowtie2-build genome.fa genome
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@Milestailsprowe: That genome.fa may be a softlink for the full genome.fa file in the "WholeGenomeFasta" directory under the "Sequence" folder. Can you check to see if that file is large?
Do yourself a favor and don't use spaces in names (external drives/files/directories). It is going to get you in trouble down the road. Anytime you feel like using a space replace that with an "_".
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Originally posted by GenoMax View Post@Milestailsprowe: That genome.fa may be a softlink for the full genome.fa file in the "WholeGenomeFasta" directory under the "Sequence" folder. Can you check to see if that file is large?
Do yourself a favor and don't use spaces in names (external drives/files/directories). It is going to get you in trouble down the road. Anytime you feel like using a space replace that with an "_".
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It appears that in one our your attempts to run bowtie you may have overwritten the original genome.fa file (you can see that genome.fa has a current "modified" date where as the rest of the files are dated from 2012/2013) .
If you have the original tar archive you should re-extract it to restore the original set of files/folders. If not, you will need to re-download the tar archive from iGenomes.Last edited by GenoMax; 06-09-2015, 05:41 PM.
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Originally posted by GenoMax View PostIt appears that in one our your attempts to run bowtie you may have overwritten the original genome.fa file (you can see that genome.fa has a current "modified" date where as the rest of the files are dated from 2012/2013) .
If you have the original tar archive you should re-extract it to restore the original set of files/folders. If not, you will need to re-download the tar archive from iGenomes.
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Originally posted by GenoMax View PostYou should align using bowtie2 index (you only specify "basename" of the index). Option to use in your case (replace full_path_to with real value) will be
Code:-x /full_path_to/Sequence/Bowtie2Index/genome
Last edited by Milestailsprowe; 06-10-2015, 06:53 PM.
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