Dear Sir or Madam,
with interest I followed up your Galaxy platform and I am planing a
Bowtie mapping with RNA-Seq data. Unfortunately the reference genome
I am looking for is not included in the drop down menu. Do you think it is
possible to add the Streptococcus suis P1/7 (NC_012925.1) genome t
Hello Douda,
This genome is sourced from build R64 (not R63), the
"NCBI_genome_source" version, with some modifications made to the
chromosome identifiers. The original data is available from SGD and NCBI
(April 2011 http://www.ncbi.nlm.nih.gov/assembly/285498/).
The chromosome identifiers b
I have RNA-seq datasets of several cell types. I want to compare alternative
splicing events between diffrent cell types. Can anyone show me the
protocol/workflow or direct me to the tutorial?
Thanks.
Jianguang
___
The Galaxy User list sho
Hello Jianguang,
The RNA-seq tutorial was just updated:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
Hopefully this helps,
Jen
Galaxy team
On 8/9/12 10:41 AM, Du, Jianguang wrote:
I have RNA-seq datasets of several cell types. I want to compare
alternative splicing e
Hello Jörg,
We can add your genome to the list to be prioritized for inclusion, but
the quickest way to use this data in Galaxy is with the "custom genome"
option.
Instructions are in our wiki (below), but there are really only two
short steps:
1 - load the fasta record into your history
2
I downloaded RNA-seq dataset at FASTQ format from SRA of NCBI. I uploaded the
dataset onto Galaxy. The dataset is paired-end. I want to split it into two
datasets (one for each end) with FASTQ splitter. But the name of the dataset
does not appear under "FASTQ reads". How should I do to solve thi
not sure but think that they need to be in fastqsanger format to be used in the
splitter. You probably have to convert them first with the groomer. But since I
am only finding out Galaxy myself, maybe wait for a more user with more
experience to answer your question.
bram
Bram Van den Bergh
Ce
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