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Recent Replies
Comment: identify unmapped regions
by
María José
▴
10
We've been analyzing chromosome coverage files for our samples and have encountered some significant gaps with no coverage at all. To inves…
Comment: Is this the correct DESeq2 design for model with interaction terms and batch eff
by
ATpoint
88k
Yes, batch and donor are usually not compatible, do one or the other. Donor (so paired analysis) is imo always preferred as most powerful, …
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Mensur Dlakic
★
29k
Binning doesn't separate any particular organisms. It separates DNA contigs based on tetranucleotide frequencies. Eukaryotes use different …
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
I can't argue with you, I'm just having problems wrapping my brain around the issue. I have wondered if the reference that NCBI BLAST is …
Comment: SE reads in fr-firststrand, fr-secondstrand
by
JourneyToAbyss
▴
250
Not trying to dig up a old thread. However, I believe Antonio is incorrect. [this](https://academic.oup.com/bfg/article/19/5-6/339/5837822?…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
Yes, the samples were collected correctly aseptically, via nurse with correct methodology. Subject 1 there are 4 different samples (shotgu…
Answer: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Mensur Dlakic
★
29k
It is impossible that *N. fowleri* has high identity to humans, or else it would be classified as a primate rather than an amoeba. Even org…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
GenoMax
152k
If possible I suggest that you find someone who can easily access your entire dataset locally and would be willing to help out.
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
GenoMax
152k
> Naegleri Fowleri Karachi NF001, which is the one identified by BLAST
BLAST should only be used for qualitative purposes for NGS data.
>…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
If you're interested enough to look at the read files yourself, I would be happy to provide them. I keep running into things that I just …
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
For the Naegleri Fowleri Karachi NF001, which is the one identified by BLAST, it's not on the NCBI genomes. It took me a long time to fin…
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
GenoMax
152k
> Yet the Naegleri Fowleri has high similarity to human
That does not logically seem correct. It is a much smaller genome when compared to…
Answer: Venn Diagram
by
zx8754
12k
Try SUMO:
- https://angiogenesis.dkfz.de/oncoexpress/software/sumo/venn.htm
Comment: Host Removal Issues Human/Dog with samples containing Eukaryotic species
by
Jon
•
0
Ideally yes, recover reads that are NOT host. Yet the Naegleri Fowleri has high similarity to human, so when I assemble the reads I don't…
Answer: Pharokka Error
by
Mensur Dlakic
★
29k
Your problem seems to be with `phanotate` version. Generally speaking, that will be best resolved if you directly communicate with the auth…
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