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Recent Replies
Answer: Feedback on Workflow
by
Asaf
8.9k
There are already pipelines in place for everything these days. If this is your first time working with NGS and the sequencing is pretty st…
Comment: Metagenomic Binning: before or after denovo assembly?
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Asaf
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binning based on what? Kraken assignment or something like that? What about the unmapped reads or reads mapped at higher taxonomic levels?
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salman_96
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Hi,
Thank you for responding.
The column Groups of interests contains information about both (other columns) condition and time_days. Woul…
Comment: high frequency subsequences
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lieven.sterck
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you might want to have a look at Kmer counting tools such as JellyFish, KAT, ntCard and such
Comment: Downloading a huge amount of Fastq files
by
davidmaimoun
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Yes sorry,
By huge I meant about **400K** genomes of salmonella.
And by years, I really don't know.
For instance, I wanted to try COBS…
Comment: DESEQ2 study design for different time points between controls and high dose sam
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ATpoint
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Yes, that so-called "full factorial" design would be the easiest while catching all the experimental factors. Check `contrasts` in the vig…
Comment: could not find function "pickSoftThreshold"
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andres.firrincieli
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Install [impute][1] and you should be fine
[1]: https://www.bioconductor.org/packages/release/bioc/html/impute.html
Comment: Downloading a huge amount of Fastq files
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Try the [ASPERA client][1] CLI.
[1]: https://www.ncbi.nlm.nih.gov/public/
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Tusharika
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Thanks! I have used the miRNA dataset from XenaBrowser and ran the Differential Expression pipeline on it using the DESeq2 Bioconductor pac…
Comment: Downloading a huge amount of Fastq files
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Would you mind adding some details. What do you download, what is "huge", why do you think it takes "years", what are your commands and wha…
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Try taxonomical classification of the reads using [Kraken2][1] or similar tools.
[1]: https://ccb.jhu.edu/software/kraken2/
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Make sure you have [UCSCtools][1] available in the mentioned location. If you are using [E-myers/rnaseq][2] , the bedgraphToBigWig functio…
Comment: could not find function "pickSoftThreshold"
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Sonia
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Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there…
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piyushjo
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Ok.
I don't think you need to care about replicates here. If you are just merging the data and your replicates form separate cluster, then…
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Here is an example how to access UniProt's REST with Python 3 with the `requests` package (`pip install requests`).
import json
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