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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Try building the index for "genome.fa" first:
Then "-x genome" would be the proper method to specify where the indices are (from your current path at least).Code:bowtie2-build genome.fa genome
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Thanks for the reply. I tried that and got a Error. Empty fasta? This is a index I downloaded from I genomeOriginally posted by dpryan View Post
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Presumably the fasta file is empty or non-existent then.Comment
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The genome.fa file? and if so how should I go about fixing that because its from the Igenome Cow setOriginally posted by dpryan View PostComment
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Well, have a look at the file. How big is it? Does it actually exist? If it does exist and seems to have a reasonable size, is it where you're telling bowtie2?Comment
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Honestly it exist and all that. Checked it out in linux and windows.Originally posted by dpryan View Post
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Given the file names, you want "-x genome", not "-x genome.fa". The documentation on this could probably be improved.
BTW, it looks like the fasta file has serious problems. It should be MUCH larger than 1KB.Comment
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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 "_".Comment
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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.Comment
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Ok untared another one and now have a 2.7gig File thanks. Should I try to align the file in the WHOLE gene folder or the one in the bowtie2 indexOriginally posted by GenoMax View PostComment
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You 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
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Fixed the wrong commandOriginally posted by GenoMax View PostLast edited by Milestailsprowe; 06-10-2015, 06:53 PM.Comment
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exit with code 1
Hi, how do you solve your problems by re-downloaded the genome from iGenomes? Do you regenerate the indexes based on the new genome from iGenomes?Originally posted by Milestailsprowe View Post
I am also running to the same issue.Comment
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