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Recent Replies
Answer: What is the best way to clean bulk RNA-seq data?
by
rfran010
▴
70
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline
by
rfran010
▴
70
Read all instructions carefully
Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software
by
rfran010
▴
70
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools
by
Bryan
•
0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA
by
rfran010
▴
70
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me.
However, there is a lo…
Comment: ATAC peak-calling: same peak ID across multiple experimental conditions?
by
rfran010
▴
70
You want to use the MACS2 score columns? You can retain these with bedtools option `-c` . This will retain the score columns from any merge…
Comment: best annotation approach for peaks
by
rfran010
▴
70
The number of regions annotated as "Promoters" is the same regardless of TSS length?
You can add this argument to annotatePeak (for mouse M…
Answer: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
It is possible that NCBI keeps the entire `nr` indexes in memory and searches against that so there is no I/O involved. NCBI now also uses …
Comment: Counting intronic reads in bulk RNA-seq
by
swbarnes2
13k
10x does give you a big flashing warning telling you what the new default is, and tells you how to redo it without that if it's not what yo…
Comment: Identification of genes involved in my pathway
by
smanzano250800
•
0
Thank you, but it doesn´t work. I´ll try GeneSCF again.
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
mohsamir2016
▴
30
Organism: gallus gallus
Genome version used: GRCg6a
Chr and Position: NC_006113.5, 24618
Ref allele: A
Alt allele: G
Genotype: 1/1 (G/G) …
Comment: Counting intronic reads in bulk RNA-seq
by
dsull
★
4.2k
Yeah, that's their assumption and also they assume that we're NOT *ONLY* interested in quantifying mature transcripts. However, for most an…
Comment: how to look for interactions between different chromosomes
by
rheab1230
▴
140
apart from tool, is there any biological mechanism for explanation of interactions between different chromosomes?
Comment: Does adding reads cause batch effects?
by
ATpoint
72k
Yes, you would process sequencing and resequencing separately and then do a PCA. I would expect no relevant batch effect here.
Comment: How to prevent reduce from being performed in GRanges during setdiff
by
hossiny
•
0
if you use `GenomicRanges::subtract(gr1, gr2) %>% unlist()` .. you'll get the `diff` without reduction
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