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Recent Replies
Comment: Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
by
ian.will
▴
10
Yep gave that a go and proceeding with the analysis. Thanks again.
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
•
0
Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using …
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
rpolicastro
12k
Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.
Comment: bwa mem hangs after a few thousand reads
by
cee28
▴
30
Here is the output with the "-v 4" flag (not showing all the @SQ comments) :
> @SQ SN:chrUn_GL000214v1 LN:137718 @SQ SN:chrUn_KI270742v1 L…
Answer: Where is the index command?
by
Michael
53k
There is a ready-made package for samtools, simply do
apt install samtools
Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴
180
Use option `-v` with value of 4 or above to help diagnose the issue:
`-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴
180
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
•
0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Comment: Generate Read counts from bam file
by
NextGenSeek
•
0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM.
The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★
16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
•
0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
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40
Hi @pratik,
Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
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520
Trying to bump this
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