updated 3 months ago by
i.sudbery
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written 3 months ago by
Parth Patel
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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
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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?
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GenoMax
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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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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
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120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters?
by
Mensur Dlakic
★
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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
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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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Mensur Dlakic
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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 …
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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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ATpoint
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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…
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