User: ATpoint

gravatar for ATpoint
ATpoint30
Reputation:
30
Status:
New User
Location:
Germany
Website:
https://www.biostars.o...
Last seen:
1 day, 14 hours ago
Joined:
2 years, 4 months ago
Email:
a*********@gmail.com

Wet-lab biologist by training, wannaba computational biologist.

Biostars Mod: ATpoint

Posts by ATpoint

<prev • 29 results • page 1 of 3 • next >
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Comment: C: How to adjust and align timepoints on x-axis in the ggplot2
... Cross-posted: https://www.biostars.org/p/409725/ ...
written 17 days ago by ATpoint30
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Rsamtools / rtracklayer creating csi index for BAM files
... I am asking this out of personal interest based on [this Biostars post][1] where OP aimed to export a BAM file with long chromosomes that do not fit into the default `bai` index, resulting in the error message one can see in that post. `export(anyBamfile.bam, BamFile(file = "exported.bam"))` After ...
rtracklayer rsamtools written 22 days ago by ATpoint30
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Answer: C: Paired t-test with DESeq2
... Others might give you a statistically-sound response but if you do not have access to the code or any details beyond doing `a t-test on your data` I would not use these results at all. Imagine a reviewer asks you at some point to clarify about the analysis strategy, what would you respond? Maybe you ...
written 9 weeks ago by ATpoint30
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Comment: C: How to find sites with H3K27me3 loss?
... Cross-posted: https://www.biostars.org/p/398094/ ...
written 3 months ago by ATpoint30
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Comment: C: Deseq2 post functional annotation for metagenome
... Cross-posted https://www.biostars.org/p/397969/ ...
written 3 months ago by ATpoint30
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Comment: C: Merging two files based on the identifier column (gene symbols)?
... Please do not cross-post. https://www.biostars.org/p/397989/ ...
written 3 months ago by ATpoint30
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Comment: C: DESeq2 unpaired RNAseq analysis
... Cross: https://www.biostars.org/p/397399/ ...
written 3 months ago by ATpoint30
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Correct use of TMM / normalization factors based on large bins
... The `csaw` package suggests to use TMM normalization based on large, e.g. 10kb, bins across the genome if ChIP-seq samples are expected to show rather global differences / composition bias is expected. As I want to use the resulting normalization factors to scale non-standard (=non `DGElist` files, ...
csaw tmm written 3 months ago by ATpoint30
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Comment: C: Problem in featureCounts file.
... Cross-posted: https://www.biostars.org/p/392402/ ...
written 4 months ago by ATpoint30
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Comment: C: Paired samples in cell lines using deseq2
... Your samples notably cluster by cell line, not by treatment. Therefore it appears unfortunate to use them as biological replicates. From a biological standpoint this quite normal for cell lines. During cell line establishment there are a lot of things changing inside the cell, particular clones star ...
written 5 months ago by ATpoint30

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