13 hours ago by
analyst
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updated 9 hours ago by
colindaven
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written 1 day ago by
skilleta0527
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updated 22 hours ago by
Yun
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written 4.3 years ago by
ofek.schnitzer
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10 hours ago by
cucindarko51
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updated 4 hours ago by
Pierre Lindenbaum
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written 5 hours ago by
awhale01
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updated 23 hours ago by
wn835166087
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written 3 months ago by
Konstantin
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updated 18 hours ago by
charles.feigin
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written 6 weeks ago by
xinrantian
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updated 3 hours ago by
Alex Reynolds
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written 4 hours ago by
Mr Locuace
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updated 18 hours ago by
charles.feigin
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written 18 months ago by
jamesymtang
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3 hours ago by
sam.himes92
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19 hours ago by
junhuili
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updated 11 hours ago by
GenoMax
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written 17 hours ago by
syedahumairagillani
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Tutorial:
CITEseq tutorial
10 hours ago by
Ming Tommy Tang
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3.6k
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updated 8 hours ago by
Istvan Albert
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written 10 hours ago by
Manuel
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4 hours ago by
mia.nahom
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updated 3 hours ago by
alex.zaccaron
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380
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written 4 hours ago by
Simone
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Recent Replies
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
•
0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Ram
41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Given files `genes.bed` and `snps.bed`, you could do something like:
```
$ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation
by
alex.zaccaron
▴
380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts
by
EK
•
0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores
by
Trivas
★
1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
•
0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores
by
Trivas
★
1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores
by
ATpoint
78k
Has phiX been spiked in to increase nucleotide diversity.
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