User: cpak1981
cpak1981 • 100
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Posts by cpak1981
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... Thanks! - I looked through the manual but not the vignette - the solution is trivial ...
written 18 months ago by
cpak1981 • 100
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... How can I write the values of `Formal class 'DESeqResults' [package "DESeq2"] with 6 slots`
```
log2 fold change (MAP): condition treat vs ctrl
Wald test p-value: condition treat vs ctrl
DataFrame with 15729 rows and 6 columns
baseMean log2FoldChange lfcSE stat ...
written 18 months ago by
cpak1981 • 100
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... Could you show the first 5 rows of your bedgraph-formatted files? ...
written 19 months ago by
cpak1981 • 100
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Comment:
C: Stringtie prepDE.py Error line 32
... What is the full path to `/SH-11/SH-11.gtf`? ...
written 20 months ago by
cpak1981 • 100
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Comment:
C: HiSAT2 segfault after long run
... @OP I believe `STAR` is less memory-hungry than `HISAT`. Could try with `STAR`? ...
written 2.0 years ago by
cpak1981 • 100
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... To most of us, there is no difference in what you've done and what you're asking for, so clarification is required. Please elaborate on what the difference is between what you've done and what you're asking for by editing your original post. ...
written 2.0 years ago by
cpak1981 • 100
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... Perhaps you're unaware of how to acknowledge answers. There should be a check mark (in addition to up/down arrows) that you as the OP can toggle on/off. ...
written 2.0 years ago by
cpak1981 • 100
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... I'm looking to download *the* latest [D. melanogaster reference genome](ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.18_FB2017_05/fasta/). In the link, I see, `dmel-all-chromosome-r6.18.fasta.gz`, which is what I think I want. But I also see `dmel-all-aligned-r6.18.fasta.gz` and I ...
written 2.1 years ago by
cpak1981 • 100
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... Does anyone know which bed columns are required for MACS2?
Is `chr start end name score strand` sufficient? (I'm guessing that MACS2 only requires `chr start end strand` but requires `strand` in the 6th position.)
Would be great to receive confirmation about this or hear if this worked for anyone ...
written 2.1 years ago by
cpak1981 • 100
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... Great, thank you for the help! ...
written 2.2 years ago by
cpak1981 • 100
Latest awards to cpak1981
Popular Question
15 months ago,
created a question with more than 1,000 views.
For stringtie (.gtf) vs ballgown (t_data.ctab) FPKM values do not match - why?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For HISAT2 rna-strandness option
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