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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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