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updated 5 days ago by
Jeremy Leipzig
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written 6 days ago by
vincenthus
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Recent Replies
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
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You did not add the screenshot.
Answer: BED files
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Alex Reynolds
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Generically via `bedmap`:
```
bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed
```
The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
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It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
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I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
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Alex Reynolds
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Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
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Alex Reynolds
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https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
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barslmn
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Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ?
by
barslmn
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Check out the 1000 genomes project.
https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase
by
Barry Digby
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1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites.
Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups
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ATpoint
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Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups
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edus_bioinfo
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To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise
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You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
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Basti
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Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file
by
Patrick
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Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades)
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taniapsduarte
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Hi,
I'm running into the same issue. Did you make it work? Or did you find an alternative method?
Thanks!
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