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Recent Replies
Comment: Adapter content in FASTQ file
by
swbarnes2
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If you seriously want to look for your sequence, you need to look for it with grep.
zgrep CTGTCTCTTATACACATCT sample.L001_R1_001.fastq…
Comment: Adapter content in FASTQ file
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Examining a few reads is not enough. If you look at the plot above ~40% of your reads are going to have adapter. So trim the data using one…
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From https://www.biostars.org/p/229379/#229380 (and now I will plagiarize):
You are not using correct separation of the file names. Sepa…
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I would even say that exact replication is close to impossible unless exact input data (count matrix), R and package versions, exact code a…
Comment: Adapter content in FASTQ file
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Adapters are in about 35% of your reads, so checking 20 out of millions is likely to not pick them up. There is also no need to do that man…
Comment: Adapter content in FASTQ file
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Hi,
Thank you for your response.
I just checked via terminal using below command for the presence of adapter sequence **CTGTCTCTTATACACA…
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These are quite arbitrary thresholds, and in mammalian genomes some regulators can bind at a much further distance. I do not have recent e…
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I don't have experience with hifiasm (and if there are settings you could tweak here), but if the species is highly polymorphic, the assemb…
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The answer is yes. In this case, the MeSH term is a more general term for the two more specific concepts. In general, mappings between onto…
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I think what @WouterDeCoster was trying to steer you toward doing is delete the line `cmd='hmmsearch --tblout output_tblout_egf --noali -E …
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You could use publication year as an upper bound, but oftentimes there is an interval of a couple of years between finishing the analysis a…
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Hello GenoMax,
I think you're right. Thank you for mentioning this paper! But I am still confused by mapping these names because it seems …
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Did they provide the counts or are you generating them yourself? If the latter, that could be the issue.
Exact replication should not be n…
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Depends on your aims, but if you are interested in how similar the transcriptional responses are between Zebrafish and your species of inte…
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Hi, the data may be found here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html
See my threads for pre-phasing and imputation, he…
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