Dear Galaxy users,
I have a tool which among other files it produces certain images in .png
format. Does anyone know if there is a way to make them appear inside the
"display data" interface?
Thank you in advance,
Efthymios Ladoukakis
_
Hi,
I'm attempting RNA-seq data analysis on *Vibrio cholerae* samples, at
galaxy main https://main.g2.bx.psu.edu/.
I was able to align transcripts using Ion Torrent's TMAP aligner. I
uploaded the BAM files and used the cufflinks tool, which gave me FPKM
scores for various transcripts. Now I want
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When using Trackster on Galaxy( https://main.g2.bx.psu.edu/root ), as
the Galaxy Wiki of Trackster
(http://wiki.galaxyproject.org/Learn/Visualization) recommend , I need
to build a track browsers for soybean because that it isn't installed
for all users. But
How does one get gene names when using cuffdiff when looking at "gene
differential expression testing" results?
I am doing some +/- exposure studies with zebrafish embryos and then
processing the 50bp single-ended fastq files through Galaxy with particular
interest in the cuffdiff readout of diffe
Hi all,
I am analyzing significant differential expressed genes for a pair of
normal V.S tumor, using Cuffdiff 2.0.2.
I noticed that by using ensemble GTF and refseq GTF, the results showed a
big difference on the number of genes being significant expressed.
For ensemble GTF, there are only 250 g
Hello,
If you used RefSeq as your reference annotation GTF from UCSC, the two
tables from the UCSC Table browser that you will most likely be
initially interested in are refGene and refLink.
These can be extracted entirely into Galaxy - as separate data files or
together as one file, using t
Hello Wei,
The contents of the reference GTF files (original, before analysis) will
probably provide some explanation. My guess is that GTF files have
different contents and are not directly comparable - RefSeq with full
transcripts and Ensembl with full transcripts + potentially partial
pred
Hi there,
I obtained two fastq files from GA paired end run. I filtered each file by
quality using fastq tool kit. Then some forward reads may be removed by low
quality whereas the reverse counterparts are OK to be remained on the other
file, or vice versa.
I want to remove those "unpaired" re
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