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Comment: How can I Extract Transposable element from a new genome assembly?
by
GenoMax
99k
Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
Comment: Trimmomatic-0.36 not finding adapter directory
by
GenoMax
99k
It is going to take as long as it takes. You need to be patient and wait until the prompt returns. Based on speed of your CPU/disk things c…
Comment: Hunting invisible characters?
by
GenoMax
99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
Comment: Can't count features with featurecount
by
avelarbio46
▴
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 necessa…
Comment: Hunting invisible characters?
by
geneticatt
▴
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
32k
Please do not delete posts that have comments/answers.
Comment: ICE normalization using JuicerTools
by
sckinta
▴
610
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
by
boczniak767
▴
740
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
32k
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
by
Mensur Dlakic
★
10k
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
★
10k
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
•
0
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…
Comment: A simple tutorial for a complex ComplexHeatmap
by
ATpoint
48k
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…
Answer: GSEA for RNA_seq dataset
by
ATpoint
48k
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…
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