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Recent Replies
Comment: How can I Extract Transposable element from a new genome assembly?
by
Philipp Bayer
6.9k
if you can transform the bed to gff (galaxy has tools for that), you could also use liftoff which wraps all of this in a pipeline https://g…
Comment: Hunting invisible characters?
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seidel
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Another way to see hidden characters is to pipe them through octal dump: `cat infile | od -c`
this will print out hidden characters, newlin…
Comment: How can I Extract Transposable element from a new genome assembly?
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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
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GenoMax
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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
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avelarbio46
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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
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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…
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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
★
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…
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