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CITEseq Alevin Seurat

8 hours ago by Ming Tommy Tang ★ 3.6k

1 result • Page 1 of 1

Recent Votes

A: difference between GSEA and Gene Ontology

Answer: Does the Minion demultiplex when basecalling?

the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?

A: Extract somatic mutations and germline mutations from variant calling files?

C: visualizing mutational data using Maftools for reference genome hg19

Answer: Ambient RNA removal method that generates whole (integer) counts

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Scholar to jared.andrews07 ★ 16k

Popular Question to hkarakurt ▴ 180

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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 awhale01 • 0

Correct I have asked those questions before.

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 sam.himes92 • 0

Yes at 5%.

Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k

Has phiX been spiked in to increase nucleotide diversity.

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