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Recent Replies
Comment: GSEA: what does 'enriched' and TOP 'X' enriched process/pathways mean?
by
jared.andrews07
★
12k
Oh, I have not used that tool. Some tools spit out scores based on some combination of p-values, gene set size, and enrichment (like enrich…
Comment: plot in r with count on y and dates on x axis
by
Papyrus
★
1.8k
What do you mean pooling? Pool the counts across all the days, and do a barplot like this example?
# Generate example data
seasona…
Comment: Most data are within Undetermined.fastq, while sample files are empty
by
swbarnes2
11k
First, you should check the first few sequences of the fastq to make sure the indices are in there, in my experience, when I use fastqs dem…
Answer: Most data are within Undetermined.fastq, while sample files are empty
by
swbarnes2
11k
> I was proposed to "restart the analyzer program (Illumina MiSeq
> Reported) and use the correct barcodes so that the reads are broken dow…
Comment: Galaxy only showing single end data for paired end data with SRR download
by
hg1
•
0
Thank you for the answer. I have written Galaxy support forum.
I am totally new to this programming and just now learning it. --split-fil…
Comment: Question on number of possible alignments
by
gannondu
•
0
The number of possible pairwise alignments is a [Delannoy number](https://en.wikipedia.org/wiki/Delannoy_number) and is equivalent to trave…
Comment: Inconsistency between Microarray and RNA-Seq results (Both were performed in the
by
ATpoint
57k
Some context would help. E.g. a plot of counts. Or the counts itself. If the difference is already in RNA-seq between analysis frameworks t…
Comment: Understanding Supplementary reads.
by
Istvan Albert
91k
chimeric reads are an odd beast, there is no "clear definition" on what a chimera is.
https://www.biostars.org/p/153461/
the way I under…
Comment: Benchmark - Comparison of Different NGS Mappers
by
kiran
•
0
![enter image description here][1]
[1]: /media/images/03419dd1-f9ef-47b8-be24-b0a4347f
Hi there,
thanks for your time.
I was just w…
Comment: Galaxy only showing single end data for paired end data with SRR download
by
Istvan Albert
91k
you should look at the command that was run for you when the data is paired the `--split-files` flag is passed to the downloading tool.
th…
Comment: blast short sequence with multiple N bases
by
Istvan Albert
91k
my feeling is that for blast to work properly you need to have a sufficient length of matching sequences. in your case perhaps try playing…
Comment: Galaxy only showing single end data for paired end data with SRR download
by
hg1
•
0
I was thinking I would get this with the download (picture)
![enter image description here][1]
However, I don't get that with the rest o…
Comment: Galaxy only showing single end data for paired end data with SRR download
by
hg1
•
0
Dear Istvan,
this is the SRR number: SRR8368419
Under single data it shows me this.
The problem is not only for that number is for most…
Answer: How to specify the depth of sequencing in ion torrent?
by
Istvan Albert
91k
The coverage of a sequencing run is the size of the genome divided by the number of total bases sequenced.
When an instrument produces i…
Answer: Inconsistency between Microarray and RNA-Seq results (Both were performed in the
by
Papyrus
★
1.8k
Do you that mean you detected a differentially expressed gene in microarrays (with *some* method), and then with RNA-seq data from the same…
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