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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
Sofia
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0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
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Istvan Albert
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Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
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mropri
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Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
Comment: Tax4Fun2 - error
by
drstalinantony28
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0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version)
1. If you are using R studio in Windo…
Answer: Tax4Fun2 - error
by
drstalinantony28
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0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version)
1. If you are using R studio in Win…
Comment: different FeatureCounts output for the same data
by
GenoMax
141k
> featureCounts alignment rate is only around 15-20%.
You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result
by
GenoMax
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> 20386810 (88.67%) aligned concordantly exactly 1 time
This result is fine.
Comment: To get p-values for the TPM
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ATpoint
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Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
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njornet
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I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
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Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided.
tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
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Hello,
you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport
cheers,
Comment: To get p-values for the TPM
by
VITALA
•
0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
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There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those.
DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
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dsull
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I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
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