Trouble downloading data from Illumina iGenomes

[anwesharry]

Is anyone else finding that they can't download iGenomes data from the Illumina ftp site? I've tried through my browser (chrome) via the cufflinks website and via an ftp client with the password and username. The error message says "connection reset". Am I doing something wrong?

[GenoMax]

Which genome are you having trouble with? I tried a couple and they seem to work.

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

[Bukowski]

I have the same issue, however I think it's to do with the work firewall. In order to get any iGenomes files I have to log in via FTP from an external machine, then FTP them again locally. I have no idea why this is the case. I spent some weeks thinking their FTP site was broken - but it isn't. Other FTP sites seem to work fine from within the work firewall, it's just Illumina's I struggle with.

[[email protected]]

I cannot download chicken files from iGenome

Dear all,
I have difficulties in downloading chicken files from iGenome site. I tried for a week but unfortunately i couldn't download them. Does anyone have these files to share with me?
Thanks in advance,
Karim

[GenoMax]

A couple of other options to try. They are not going to be as well integrated as iGenomes since you will need to make the aligner indexes etc.

1. From NCBI.

Sequence: ftp://ftp.ncbi.nlm.nih.gov/genomes/G...romosomes/seq/ You will have to get the sequence files and cat them together.

Annotation: ftp://ftp.ncbi.nlm.nih.gov/genomes/Gallus_gallus/GFF/


2. UCSC table browser from UCSC: http://genome.ucsc.edu/cgi-bin/hgTables.

Select "clade" = vertebrate and chicken as "genome". There is some basic help available at this link: http://genome.ucsc.edu/goldenPath/he...ablesHelp.html

You will have to do two passes. One pass download the sequence. Second pass get the annotation in GTF format.

[[email protected]]

my cuffdiff outputs

Dear Genomax,
Many thanks for your advice. I have downloaded reference genome and transcriptome from Ensembl: ftp://ftp.ensembl.org/pub/release-79...us_gallus/dna/
And successfully used these files in analyzing my RNA-Seq data using Tuxedo Software Suite. My problem is with cuffdiff output files. These files do not have ensembl gene ids. The first row of gene_exp.diff file is as below:
test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
XLOC_000001 XLOC_000001 - 1:1734-16503 As He OK 2.33458 2.12714 -0.134246 -0.256022 0.77365 0.99974 no
I have learnt from some seqanswer threads that in order to have cuffdiff outs with reference gene ids, I should have used iGenome files (although I am not sure yet). So, I want to analyze my data using iGenome files and compare with my previous results. Could you or other members help me to solve this problem.
Thanks for your time and consideration.