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Recent Replies
Comment: Longitudinal analysis of subpopulations: which approach is better?
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ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
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jkbonfield
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1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
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80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers
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christopher medway
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You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
Comment: ChIP-seq datasets: input samples omitted?
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i.sudbery
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Fascinating!
We also use inputs when doing metagene to protect against those situations where regions up or downstream of our metagene al…
Answer: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
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i.sudbery
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See the section on non full rank design matrices in the DESeq2 manual.
In this case your problem is that healthy and 0dpi samples are e…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Can you clarify what you mean by "100% of reads pass cutadapt, even though 70% of reads contain adapters and get trimmed. " did you set a m…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
I don't follow your argument for distinguishing between genomic contamination and freud. A data set being bad in terms of genomic contamin…
Comment: What does it mean single base resolution in sequencing?
by
jinyu
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Thank you for your detail and great explanation. I do need more time to understand these. And there is still something compuzzling me. For …
Answer: Is it possible to bulk download files from GEO repository?
by
atharvakarkare14
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Try using this library [GEOparse][1]
[1]: https://github.com/guma44/GEOparse
Answer: How many reads for WGS Sequencing?
by
Ruqaiya
•
0
OK. Problem solved. The problem was from my end.
Thank you both for helping !!
Comment: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★
27k
Appreciate the suggestion, but that ship has sailed and reached the other shore. This happened 10+ years ago. To the best of my knowledge n…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
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30
Files are not opening in any of the computer (ubuntu/windows). I rereun snpEff annotation but still output html files are having missing im…
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴
30
I reinstalled nodejs:
> sudo apt-get install nodejs
Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
Prash
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Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
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