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Comment: Can't count features with featurecount
by
avelarbio46
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10
I'm not sure about three things:
What does -M and -O do exactly that could benefit in my case?
Why should I specify -t if I don't necessari…
Comment: Hunting invisible characters?
by
geneticatt
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120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters?
by
Mensur Dlakic
★
10k
You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing:
dos2unix i5R.txt
If an error pops …
Comment: RNA seq analysis; two samples
by
Ram
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Please do not delete posts that have comments/answers.
Comment: ICE normalization using JuicerTools
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sckinta
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Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
Comment: How to verify putative miRNA
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boczniak767
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Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well.
[1]: https://j…
Comment: R - A bioinformatic analysis programming language for NGS
by
Ram
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Because this is a plain copy-paste from the novogene page, it has numbers (pointers to specific references that the source has), but not th…
Comment: X amino acid in ensembl
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This is correct. `X` means any amino acid. Most substitution matrices apply identical penalty (`-1`) when any amino-acid is aligned with X …
Answer: differential expression analysis
by
Mensur Dlakic
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I think the numbers you cite are the most extreme values that people will still accept. In most cases I would go for lower p-values (at lea…
Comment: Trimmomatic-0.36 not finding adapter directory
by
willbrown
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The two reads are roughly 23GB each, the only other large output file generated in my last attempt was the trimlog file, which was only 1.5…
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You always normalize data before z-scoring it. The Z-score just calculate like the "deviation" of every sample from the mean of all samples…
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I tried to explain my understanding of (f)GSEA and why one should use all (expressed) genes here over at this Bioc post:
https://support…
Comment: Trimmomatic-0.36 not finding adapter directory
by
willbrown
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I have re-run Trimmomatic for a few hours now, but still no prompt from the terminal. I included '-threads 8' and so expected it to be some…
Comment: How to perform multiple alignment using MAFFT?
by
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Ok thanks a lot. I used the `system(paste0("printf \"\n\" >> Alignment_output/temp.fa"))` after the samtools command and the last command i…
Comment: How to perform multiple alignment using MAFFT?
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Ram
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There are probably a few files that do not have a new line character before the End of File character (the last visible character is a sequ…
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