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C: why GATK makes things more complicated ?
Answer: RNA-Seq analysis
Comment: UMI-Tools knee-method has great influence on the results of white list
Answer: RNA-Seq analysis
Answer: salmon with long read
I cannot download VG in any way
Comment: I cannot download VG in any way
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Comment: bcl-convert cannot create output directory structure at the path specified
by
marco.barr
▴ 130
I've never received this error before.. but you could try checking the permissions
Answer: How do i calculate the mean of triplicates in a data.frame based on pattern?
by
gglim
▴ 140
``` library(dplyr) df %>% rowwise() %>% mutate(p767.AM = mean(c_across(contains("AM")))) ``` Maybe this is what you're looking for?
Answer: RNA-Seq analysis
by
Michael
54k
I think the situation you are finding yourself in is quite common. On a general note, as you are at the beginning of your PhD program, you …
Answer: RNA-Seq analysis
by
Nat.Nataren
▴ 30
We'll need a lot more information to help, you haven't given us much to work with. What organism are you working in? What is the experi…
Comment: Cut&Run and heatmap
by
gglim
▴ 140
I'll take a look at these peaks in IGV with the signal files and set a threshold for filtering.
Comment: NCBI vs Ensembl - Ortholog genes Information
by
José
▴ 10
Thanks for the answer and the advice.
Comment: NCBI vs Ensembl - Ortholog genes Information
by
José
▴ 10
Thak you so much for your answer and advice.
Comment: coding and non-coding region of the viral genome
by
dthorbur
★ 2.0k
You also have intronic regions between exons that also count as non-coding regions. Psuedogenes and non-coding RNAs too. I'm sure there are…
Comment: samsift can't find the AS tag to filter a bam file generated using bowtie2
by
Pierre Lindenbaum
162k
what is AS ? an attribute in a SAM record? Are you sure this is the way to access an attribute : `-f 'AS>94'` . Otherwise, just use `samt…
Comment: Filtering reads that map to both references
by
Pierre Lindenbaum
162k
see related : https://www.biostars.org/p/274183/
Comment: I cannot download VG in any way
by
dariober
14k
Downloading the binary as GenoMax (and the vgteam) suggests is most likely the best option. For the record, `git clone --recursive https://…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
It was 10X data, and I processed it using Seurat. Then, I came to the point of Pseudobulk using DESeq2. Does this mean I have to check whi…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
We recommend alecin where it supports the kit you are using. As far as I'm aware it doesn't support custom read geometry yet, but does supp…
Answer: NCBI vs Ensembl - Ortholog genes Information
by
b.contreras.moreira
▴ 200
Hi José, orthology inference is tricky and that's why the <https://questfororthologs.org> consortium has been comparing **graph-based** an…
Comment: Manual Polygenic Risk Score calculation
by
ashaneev07
▴ 20
Hello, Did you calculate the score successfully? I'm also facing issues with prs score calculation.
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