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Answer: Grouping datasets in Seurat
Best tool to find potential TF binding sites within a specific DNA sequence?
Comment: RNA seq analysis
Answer: getting exon coordinates
Comment: getting exon coordinates
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: getting exon coordinates
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Comment: How can I calculate the OS of each patient?
by
ATpoint
82k
Please be specific. Which TCGA subset, what did you try? Show code.
Answer: mitochondrial genome assembly pipeline
by
shelkmike
★ 1.2k
A good tool for mitochondrial genome assembly is GetOrganelle (https://github.com/Kinggerm/GetOrganelle)
Comment: getting exon coordinates
by
Ram
43k
Please do not use `bioinformatics` as a tag unless your post in about the field of bioinformatics itself.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
I've removed unneccessary tags - `meta` and `how-to` don't apply to this post at all, and the `forum` tag is not in use anymore.
Comment: Difference in number of reads when using duplex and simplex base calling with Do
by
GenoMax
142k
I assume you have posted this in nanopore community and/or on the dorado issues page on GitHub. Please come back and post an update once yo…
Comment: Annotating file using bcftools
by
kl
▴ 10
Do you know if there is a way to leave chr:pos in ID if there is no matching rsid based on chromosome and position, as variants have been r…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
Jeremy Leipzig
22k
We get this question like clockwork every 6 weeks. I'll say it one more time: **A freeze is a freeze.** Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Thanks very much for your feedback! I will take all those things in consideration once I start the analysis! Just out of curiosity, do yo…
Answer: getting exon coordinates
by
ben@f
▴ 20
A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest and a text file with Gene…
Comment: getting exon coordinates
by
Pierre Lindenbaum
161k
https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc... <!-- How …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
I would have thought `needle` from EMBOSS would be the option to use.
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
ok, then you should add the donor information to the PCA analysis. First create a separate dataframe for the donors, then add with `factor`…
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 180
If you are willing to do some coding I think <https://github.com/smarco/WFA2-lib> is among the fastest global aligners, the repo has C++ ex…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
GenoMax
142k
There is an API that you could try: https://www.ebi.ac.uk/pride/markdownpage/prideutilities
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
Pierre Lindenbaum
161k
thanks. looks interesting but it's broken. the Firefox console shows a 404 for https://www.ebi.ac.uk/pride/ws/archive/v2/peptidesummary?ke…
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