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Recent Replies
Comment: The inchworm process failed. Trinity running error.
by
GenoMax
129k
The solution is noted in the error output
> You'll need to either reduce the size of your data set or run Trinity
> on a server with mo…
Answer: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.8k
In addition to the stratified analysis above, which you might consider framing as a LRT through DESeq2, another approach is to conduct a pr…
Comment: including samples for which group is unknown to help adjust for another variable
by
Vincent Laufer
★
2.8k
one gets that message from time to time in reasonably powered datasets.
ill write out a second approach right quick
Comment: including samples for which group is unknown to help adjust for another variable
by
pilargmarch
▴
80
Thank you for your response! I didn't think of doing the stratified analysis because of the small sample sizes, but it is worth trying. Com…
Comment: ggsave() bug in ggplot2?
by
Medeea
•
0
sorry, I was actually thinking that maybe you meant this
$ file Figure1.jpg
Figure1.jpg: JPEG image data, baseline, precision 8, 2500x150…
Comment: Single Cell Rna Seq Using BD Rhapsody
by
GenoMax
129k
Good to know. I was unaware that `kb` can understand BD data. I was under the impression that one needed to use BD software for the initial…
Answer: Data is not displaying in DATABASE......error is not showing in IDE
by
Dr William Klubinski
▴
30
It seems error might be due to a problem with the way u construct SQL query. the $sql variable isn't being assigned a value in some scenari…
Comment: how to run FacetsSuite wrapper scripts on command line
by
GenoMax
129k
Unfortunately the vignette is not very clear. It appears that you need to compile a program called `snp-pileup` and have it available in th…
Answer: how to sort a fasta file
by
Dr William Klubinski
▴
30
Using Python:
This code reads your FASTA file, stores the entries in a dictionary and writes them back to a new FASTA file in a sorted o…
Answer: BioInformatics, Software
by
Dr William Klubinski
▴
30
**Galaxy** is very common but you cannot cluster data in Galaxy (i.e. Seurat or SC3 for clustering and dimensionality reduction), so you ma…
Answer: Single Cell Rna Seq Using BD Rhapsody
by
Dr William Klubinski
▴
30
In general, the course of action should go as follows. Use FastQC to generate quality reports on your raw sequence data (Go to "NGS: QC and…
Comment: NarrowPeak format -Peak field
by
aaronlogsdon2001
•
0
Hi ATpoint - quick question. In my mind, 0-based means counting from 0. So if the peak value column shows 50, the summit is 52 (1 + 51), no…
Comment: Single Cell Rna Seq Using BD Rhapsody
by
dsull
★
4.2k
I think a good solution would be kallisto/bustools (or other solutions that work, like STARsolo or alevin-fry).
E.g. For kallisto/bustools…
Comment: DEGseq for multiple samples
by
Basti
★
1.5k
logFC and p-values are results of a differential analysis between the groups, it does not exist in the context of individual samples
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