User: jordi.planells
jordi.planells • 230
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Posts by jordi.planells
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... Sorry to bother with this simple question, but does this apply as well for p_value and p_adjusted of DESeq2 output??
Thanks! ...
written 8 weeks ago by
jordi.planells • 230
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... You can also try `bedtools intersect`. See [here][1] for more details
[1]: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html ...
written 9 weeks ago by
jordi.planells • 230
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Comment:
C: SRA tool kit
... If you install it with conda you won't have to configure anything ...
written 3 months ago by
jordi.planells • 230
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... In public data there are only 2 files (R1 and R2) because the concatenation (the cat command) of the different lanes has already been performed.
Recap:
To merge the different lanes, use `cat`
To merge different bam files (for example several replicates) use `samtools merge` ...
written 3 months ago by
jordi.planells • 230
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... Hi! I think what you have there is 2 fastq files for the same sample, each one coming from a different sequencing lane (note that some of the files have L001 and some others L002). What you need to do is to concatenate the sequencing lanes into one file and then align with the resulting file.
...
written 3 months ago by
jordi.planells • 230
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... Have you realigned allowing multimappers? If you run featureCounts on the same bam file (in which you have filtered out the multimappers) won't do any difference. I have been using featureCounts with and without the -M flag and definitely I see a difference in the quantification. I can suggest you t ...
written 3 months ago by
jordi.planells • 230
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... As far as I know, salmon takes multimappers into account, maybe there you find the difference. Could you align with STAR allowing multimappers, quantify with featureCounts with -M flag and get the correlation again? I am very curious on how this will behave ...
written 3 months ago by
jordi.planells • 230
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... In case anyone faces the same problem, I will paste the code I used to get the plot.
# Subset the dataset into different knockdowns
A = com_sig.df[com_sig.df$Knockdown=="A",]
B = com_sig.df[com_sig.df$Knockdown=="B",]
C = com_sig.df[com_sig.df$Knockdown=="C",]
# Compute the ...
written 3 months ago by
jordi.planells • 230
0
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... Thank you so much! This work smoothly! I am pasting the code with the answer and closing the question ...
written 3 months ago by
jordi.planells • 230
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... One p-value for each biotype (or boxplot) in each facet. In other words, if I have 6 boxplots per facet, I should get 6 p-values per facet ...
written 3 months ago by
jordi.planells • 230
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