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Forum:
Nextseq for analysts
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Popular Question to
pandey.gaurav
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Recent Replies
Answer: GSEA for RNA_seq dataset
by
Zhilong Jia
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Using all genes with signed P-value to rank genes, where the sign is from LogFC.
and `GSEAPreranked` module in GSEA.
ref: [Gene Ranki…
Comment: How can I Extract Transposable element from a new genome assembly?
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Philipp Bayer
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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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Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
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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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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?
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geneticatt
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Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters?
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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 …
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Please do not delete posts that have comments/answers.
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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…
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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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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 …
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