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Recent Replies
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
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Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
•
0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
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890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴
40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★
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Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★
27k
It is a good idea, though I don't see how it would work in practice.
I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴
890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/
https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
•
0
Sorry for the delay in my answer, I got sidetracked.
I am using
```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE```
bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
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10
We just developed a R package to tackle this problem.
Do you have stranded or unstranded RNA-seq data contaminated with gDNA?
If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report
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GenoMax
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`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed)
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swbarnes2
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Cross posted here (including the code used to make up the counts):
https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
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swbarnes2
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RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
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