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Recent Replies
Comment: Annovar using R package
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Pierre Lindenbaum
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duplicate of your previous question: https://www.biostars.org/p/9592646/
why using R when there are shell-based tools like VEP ? slivar , …
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Lissa Cruz Saavedra
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Hi
I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
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swbarnes2
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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
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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
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biochugs
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Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
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Jeremy
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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
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DKA
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I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
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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
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It is a good idea, though I don't see how it would work in practice.
I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
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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
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@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
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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
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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
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haibol2017
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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…
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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…
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