(no subject)
by Xiangming Ding
Hi galaxy
I am a new user of galaxy. i met a problem and didnot find similar
question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
galaxy through UTL method. The file is around 800M. However after
uploading, the FASTQ file was just around 2M. So I wanted know whether
it is possible to upload a large file to galaxy through URL method? or
I should download the file to my pc and then uploading to galaxy
through FTP method.
Thanks
xiangmimg
10 years, 8 months
Bed to Wiggle?
by shamsher jagat
Is there an option to convert Bed file to wiggle file in Galaxy?
Thanks
10 years, 8 months
BWA install problem
by Christopher Callaway
Hi,
I am trying to run Galaxy locally and downloaded BWA but I can't get it to run. Do I have to use 0.5.6 or can I use 0.5.9? The make command does not work with ver. 0.5.9.
Thanks,
Christopher W. Callaway
University of Utah
Dept. of Pediatrics
Division of Neonatology
417 Wakara Way
#2222
Salt Lake City, UT 84108
10 years, 8 months
Question about Cuffdiff
by Alessia D
Hi,
I am confused about the first line in cuffdiff (using Galaxy on the cloud,
not sure if it's different for local instances). It reads:
Transcripts:(choose a file)A transcript GTF file produced by cufflinks,
cuffcompare, or other source.
What file should I load here? I have 4 groups of 2-4 replicates each that
I am comparing, and am using the "grouping" option that follows. Should I
use one of the files produced by cufflinks? If so, which ones? Or should
I rather use the GTF file of RefSeq genes from the UCSC database?
Thx!!A
10 years, 8 months
Removal of duplicates and Cufflinks usage
by Lizex Husselmann
Hi All
I've started analyzing my RNA-Seq data for two time points: Day0 and Day4 for control and treated. I've done aligning the data to the reference genome using Tophat. I've removed duplicates from the data sets. Could somebody please tell me, how important is it to remove duplicates and how will it influence my results if I don't remove?
I want to start with Cufflinks all the way through to Cuffdiff. Where do I start since there are just so many options (in the manual) to choose from? What do I look for?
Kind regards
Lizex
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10 years, 8 months
Re: [galaxy-user] Help with analysis
by Alex Daffornel
>
> Brand new galaxy user here.
>
> I ran an RNA-seq Illumina experiment in which I compare cells from wild
> type animals and cells from animals that have a deletion in a splicing
> factor. Now I have my data in fastq format and need to do analysis to
> figure out which transcripts are changed and how (see below). Problem is, I
> have no idea whatsoever what to do.
>
> Can someone be so kind and write down a basic outline of analysis to
> follow?
>
> My understanding from what I've been reading online is that once you have
> fastq files you
>
> 1. Use FASTQ Groomer to convert to Sanger format
>
> 2. Evaluate the quality with FASTQ Summary Stats (and get boxplot of data)
>
> 3. Trim reads if their quality doesn't look good
> What is considered "ok" quality? A score above 20? Is that the
> mean score or the absolute score? How do I trim based on score only those
> reads that have a low q score? (can I?)
>
> 4. Map the reads
> What mapping software do you reccomend? BWA or Bowtie? Or Tophat?
> What next?
> Let's say that anything after the trimming is very fuzzy.
>
>
> The questions I am interested in are
> - What transcripts are upregulated / downregulated in mutant vs control ?
> (I have 3 replicates of each)
> - Are there introns that are retained in mutant (but not or less in
> control)?
> - Are there exons that are excluded in mutant (basically, I want to at
> patterns of alternative splicing..)
>
>
> Sorry for the very long message, but I have no idea who else to ask.
>
> Thanks!!
>
>
>
>
>
>
>
10 years, 8 months
cufflinks error
by jh yu
Dear all:
Recently I am using cufflinks to analyze differential expression between different conditions, but when using cufflinks an error occurred:
An error occurred running this job:cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat
Error running cufflinks. [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this
However, when I used the same parameters to analyze another file, it worked well:
19,904 lines
format: gtf, database: rhodRHA1
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat
The only difference is the size of each file, the failed one input file is 23 G, while the succeeded one input file is 3.5 G, is the size causing failure?
Thank you in advance.
Best wishes!
Sincerely, Jinhai YU
Jinhai YU, Ph.D Candidate
010-64888521
Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
10 years, 8 months
cufflinks set parameters
by dongdong zhaoweiming
Hi,
It's the first time for me to use cufflinks in galaxy, two choices confused me as follows:
Perform Bias Correction:
No Yes
Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
Set Parameters for Paired-end Reads? (not recommended):
No Yes
what is the Bias correction and how does it work? And for "set parameters for paired-end reads? (not recommended)" ,what would be important difference between recommended and not recommended?
Thanks a lot!
dongdong
10 years, 8 months
data format
by Klaudyna Borewicz
Hi,
I would like to use Galaxy to run LEfSe, but I don't know how to get
the data into tabular format that is required
(http://huttenhower.org/galaxy/tool_runner?tool_id=LEfSe_for). My data
is 454 fasta files that I was analyzing with RDP to get the
classification. It works fine, I get .txt file that i can load to
Galaxy, it looks like this:
norank Root 37646
unclassified_Root 9
domain Bacteria 37637
unclassified_Bacteria 5998
phylum OD1 0
unclassified_OD1 0
genus OD1_genera_incertae_sedis 0
phylum BRC1 0
unclassified_BRC1 0
genus BRC1_genera_incertae_sedis 0
phylum Deferribacteres 0
unclassified_"Deferribacteres" 0
class Deferribacteres 0
unclassified_Deferribacteres 0
order Deferribacterales 0
unclassified_Deferribacterales 0
family Deferribacterales_incertae_sedis 0
unclassified_Deferribacterales_incertae_sedis 0
genus Caldithrix 0
family Deferribacteraceae 0
unclassified_Deferribacteraceae 0
genus Calditerrivibrio 0
genus Mucispirillum 0
.....
but i need to have the labels in a hierarchical organization and I
cannot find the way to get it to work. Please let me know if you have
any suggestions, or maybe RDP is just not the way to go.
Thank you and hope to hear from you soon,
Klaudyna
--
____________________________________________________
Klaudyna Borewicz M.Sc, B.Sc
Department of Veterinary and Biomedical Sciences
University of Minnesota
1971 Commonwealth Ave.
St. Paul, Minnesota 55108
Phone: (612)624-6226
FAX: (612)625-5203
10 years, 8 months
fastx reverse compliment failed - gzip: stdout: Broken pipe
by Lucinda Lawson
Hi all,
We are running Galaxy on an Ubuntu 11.10 computer (5 TB, stripped,
etc.). We are assembling a small genome (110 Gb). Our dataset isn't
directly uploaded, but is accessed from a directory (if that matters).
Everything went fine through the FASTQ Groomer, but when we ran
Reverse-Compliment, we got the following error:
fastx_reverse_complement: writing quality scores failed: File too large
gzip: stdout: Broken pipe
Any help that you might have would be greatly appreciated! Thanks!
-Lucinda
10 years, 8 months
