[dinesh21.ksd]

guys, now i am working on earthworm RNA sequencing. i need to study the gene expression of earthworm RNA seq.

for gene expression analysis i use tophat and cufflinks.

(ref: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks)

i am already install all the software (tophat, cufflinks, bowtie, CummeRbund). for running these software i need reference genome.

in that above ref. paper reference genome download via their website. but i am not able to download the reference genome. they ask username and password.

so kindly help me to download the reference genome.

then also help me to choose the reference genome which one is suitable for earthworm.

[mastal]

guys, now i am working on earthworm RNA sequencing. i need to study the gene expression of earthworm RNA seq.

for gene expression analysis i use tophat and cufflinks.

(ref: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks)

i am already install all the software (tophat, cufflinks, bowtie, CummeRbund). for running these software i need reference genome.

in that above ref. paper reference genome download via their website. but i am not able to download the reference genome. they ask username and password.

so kindly help me to download the reference genome.

then also help me to choose the reference genome which one is suitable for earthworm.

I find I can download the pre-built indexes without being asked for a username or password, from either the Bowtie, Bowtie2, or Illumina iGenomes web pages, links given below.

http://bowtie-bio.sourceforge.net/index.shtml

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

http://support.illumina.com/sequencing/sequencing_software/igenome.html

You can always build your own index.

I think your problem is going to be that the only worm reference genome on these web sites is C. elegans, which is probably not closely enough related to
whichever earthworm species you are working with.

If you can't find a closely-related reference genome, you can always try de novo transcriptome assembly.

[GenoMax]

guys, now i am working on earthworm RNA sequencing. i need to study the gene expression of earthworm RNA seq.

for gene expression analysis i use tophat and cufflinks.

(ref: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks)

i am already install all the software (tophat, cufflinks, bowtie, CummeRbund). for running these software i need reference genome.

in that above ref. paper reference genome download via their website. but i am not able to download the reference genome. they ask username and password.

so kindly help me to download the reference genome.

then also help me to choose the reference genome which one is suitable for earthworm.

Dinesh: First a suggestion. Start a new post for a question that is not directly related to a thread even if the title of the thread appears to be similar to what you are asking.

You are the earthworm expert (relatively speaking) so you need to include additional information about which earthworm species are you specifically looking at/for.

Here is an example earthworm genome that may or may not work for you.

http://badger.bio.ed.ac.uk/earthworm/home/download

If the genome you are looking for is not available publicly (e.g. Amynthas) then you may need to assemble a transcriptome yourself using RNAseq data.

[dinesh21.ksd]

tnx for the reply. i try ur suggested website http://support.illumina.com/sequenci...e/igenome.html. but i cant download in our campus internet because of some security problem.

i try to ask in my university and get a permission to download that file .

once again thank u