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8.7 years ago
BDK_compbio ▴ 130
I am getting some error while running tophat2. I used bowtie2 for building indices using the following command
bowtie2-build --large-index <refrence> <output directory>
It generates indices with suffix bt21 (instead of bt2). Bue when I am running tophat it is giving me following error
Could not find Bowtie 2 index files (.*.bt2)
Which version of tophat2? I think only the most recent version supports large indexes (it doesn't actually say in the release notes).
I am using tophat/2.0.12 which is the latest version I guess.
It appears that your post has been cross-posted to another site: SEQanswers
This is typically not recommended as it runs the risk of annoying people in both communities.
Thanks for the suggestion. I posted on both sites thinking that I would get quick answer.
I ran it like
where hg19 is base index prefix and hg19refseq.fa is reference sequence
in the given directory
And TopHat2 always runs very well using them.
I also ran like that, but it gave me the following error
That's why I tried
--large-indexoption. I am now using BWA-MEM and STAR instead of bowtie+tophat
May be, you try with TopHat 2.0.8 version which works for me.
I am using tophat 2.0.12
Actually the reference file is too large, so bowtie-index won't work if you don't use
--large-indexoption. The current version of tophat does not support the large index. Did you use
--large-indexparameter? Maybe the size of your reference file is not large enough.
which reference genome you are using?
I did with Human, Chimp, Gorilla, Rhesus, cynomolgus, mouse etc, trference genome and never face any problem
None of those have a large enough genome to require large-genome support, which is good since tophat can't yet do that.
I am using a prebuild index (.bt2 files) of hg19 for bowtie2, but every runs has an error that says it is too large
I know hg19 is too large, and even the fastQ file I am using is also large. But is not there anyway out to run bowtie 2 on this?
Firstly, please start a new thread for things like this rather than posting questions as a comment.
Secondly, you can certainly use bowtie2 for hg19, you just need to use a computer with more RAM (as the error message said).
Oops sorry for not starting a new thread. I am new here and somewhere it said, for discussions use the comment tab!
OK so I need more RAM. How much is least RAM required to run a mapping for hg19? My PC has 8GB RAM
I am quite new to this, so please consider this as a genuine doubt! And yes I will make sure I post doubts as new threads from next one!
I'm a little surprised that that's not enough, though I suspect you have other things running. I would expect that 12 gigs would suffice.
Thank you for the reply! Even I was wondering why? I tried closing all other programs and running it again! No luck!