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Recent Replies
Comment: Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
by
ian.will
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Yep gave that a go and proceeding with the analysis. Thanks again.
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
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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
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Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.
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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…
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There is a ready-made package for samtools, simply do
apt install samtools
Also, your screenshot shows you are using the root account…
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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…
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Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
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Thank you, I really appreciate your insight! I will look into the dropouts I have.
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Are you analysing RNA or DNA heteroplasmy levels?
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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 …
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edgeR *is* an NB-GLM.
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Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
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its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
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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…
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Trying to bump this
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