User: Morris_Chair

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Morris_Chair120
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Posts by Morris_Chair

<prev • 106 results • page 1 of 11 • next >
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Comment: C: Merge DEseq and Cufflinks outputs
... I did compared DESeq2 vs Tuxedo suit, (In general bioinformaticians suggest to don't use use cufflinks but the updated pipeline, HISAT2 > StringTIE > Ballgown). Once you get your results, removed the ID with high p-value for each output, then you can use the Venny Graph to see what is common a ...
written 1 hour ago by Morris_Chair120
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Comment: C: Biological replicates and depth seq
... The two groups exist because they are two different cell lines, means a different genetic background. What really matters to me is that the condition for each cell line have to be close which in the heatmap differs based on the number of genes selected Thanks ...
written 16 hours ago by Morris_Chair120
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Comment: C: Biological replicates and depth seq
... Hi ATpoint, Here you can see the PCA plot, I'm repeating one condition (the green on the right side) because there is too much variance. This are two different cell lines well separated Thank you ...
written 1 day ago by Morris_Chair120
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Comment: C: Biological replicates and depth seq
... sure WonterDeCoster you're right, but Kevin is not like others .. (I'm kidding), sorry if violate the rules .. ...
written 1 day ago by Morris_Chair120
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Comment: C: Biological replicates and depth seq
... Kevin your silence scares me :D ...
written 1 day ago by Morris_Chair120
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Comment: C: Can you detect novel (non-coding) transcripts using Salmon and the hg38 transcri
... Thank you Kristoffer :) ...
written 2 days ago by Morris_Chair120
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Comment: C: Biological replicates and depth seq
... Hi Charles, My samples are from the same experiment, How would you focus on high more expressed genes? still using DESeq2? Thank you for you answer ...
written 4 days ago by Morris_Chair120
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Comment: C: Biological replicates and depth seq
... Hi Kevin, The experiment consists of treating the cells in 4 different conditions (knock-out) where each condition has a biological replicate, then in total I have 8 sample. I used two different cell lines treated the same way so at the end I have have 16 samples. The script used is the following: ...
written 4 days ago by Morris_Chair120
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Biological replicates and depth seq
... Hello, everyone I have a question about samples replicates of RNA sequencing depth. When I run the heatmap in my set of experiments with DESeq2, the replicates are not always together and the position can change based on the number of genes that I consider (100 or 1000). I noticed that this effec ...
deseq2 rna-seq written 4 days ago by Morris_Chair120 • updated 4 days ago by Charles Warden7.0k
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Comment: C: Ballgown Error in file(file, "rt") : invalid 'description' argument
... Hello I have a simple question, I want to reproduce this pipeline with my own data but it's not clear to me what the "ERR" in samplePattern is, I mean, is it the filepath of the single folder containing the .gtf created? I would appreciate this clarification thank you ...
written 4 days ago by Morris_Chair120

Latest awards to Morris_Chair

Centurion 4 days ago, created 100 posts.
Supporter 4 months ago, voted at least 25 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For Bamfile first step analysis

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