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Recent Votes

A: What is 'reverse' blast, and when to use it?

A: FindAllMarkers pct1 and pct2

search for low coverage regions on bam file

Comment: How to pair TCGA bam files with no properly paired reads?

Answer: EDAseq, edgeR libraries cannot be installed in M2 mac

Answer: Changing the format of a column in a file

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Recent Replies

Comment: Find ~1 Mb regions of genome that are shared by two or more WGS samples? by 5heikki 10k

Hi, I thought you were working with bacterial genomes. Sorry, can't help really..

Comment: HEXplorer: Scanning splice site sequence surroundings for splice enhancing/repre by PedroBarbosa ▴ 20

Hi, Thanks for the tool, but the link you provided does not work. Was the tool discontinued ? Best, Pedro

Answer: Fasta headers column spilt or selection by young_bioinformatician ▴ 170

awk '{print $3}' input > output

Answer: Fasta headers column spilt or selection by antmantras ▴ 20

cat myfile.fasta | grep ">" | awk -F " " '{print $3}' This will print the file, pass to the grep command where headers (starting wit…

Answer: SEURAT : loading via h5 file and applying min.cells and min.features by ZheFrench ▴ 480

Ok `Read10X_h5` did the trick. fileh5 <- glue ("{outdir}/filtered_feature_bc_matrix/filtered_feature_bc_matrix.h5") seurat.obje…

Comment: variant analysis using Freebayes by young_bioinformatician ▴ 170

We know that false positive issue happens in variant caling tools. You can read benchmarking papers about this. Nevertheless, I would consi…

Comment: EDAseq, edgeR libraries cannot be installed in M2 mac by Gordon Smyth ★ 5.0k

Yes, that's right. But the point of the bioc-devel post that I linked to is that, starting from today, you shouldn't need to install the in…

Comment: Basic PRS question by tacrolimus ▴ 100

I have a set with both

Comment: Beta-matrix. Differential methylation analysis by Basti ▴ 790

Your question is very vague because everything depends on your data. Where does it come from ? How was it processed ? From which platform a…

Comment: Difference between (~group) and (~0+group) in design matrix edgeR by Basti ▴ 790

I suggest you to read this guide to creating design matrices : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873980/.

Comment: Changing the format of a column in a file by munaj86 ▴ 30

Thanks for this. I have a script that do this job but when I run it it gives me an error so I decided to look for a simple way rather than …

Comment: EDAseq, edgeR libraries cannot be installed in M2 mac by Sakib Salam • 0

The problem is resolved by installing the intel version R. Thanks!

Comment: how can i interpret cox multivariate analysis result by Sarah Zac ▴ 20

Thank you a lot !

Answer: MLPE vs ML in lmer (landscape genetics) by stacy_biology97 • 0

They are the same thing.

Comment: How to code phased vcf genotypes into numeric sequence by caredevil • 0

Thank you for your reply. I think my question is pretty self explanatory and there is no need for further information. But as requested…

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