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Recent Replies
Comment: How to plot chipseq peak relative to TSS for some genes ?
by
Carambakaracho
★
2.5k
dplyr's [group_by + count][1] are your friends:
```R
library(tidyverse)
test <- tibble(
gene = c(1,1,2,2,2),
peak_ldist_tss = c(10, 3…
Comment: Installing stringr after upgrading from Ubuntu 18.04 to 20.04
by
tul66893
•
0
Thanks for the reply! When I run `install.packages("stringr", repos='http://cran.us.r-project.org')`
> > installing *source* package ‘stri…
Comment: Why does Kraken2 not produce taxon percentages with --report flag?
by
DNAngel
▴
140
Yep! I got it to finally work when removing the --use-mpa-style. I think that change in format was interfering with the report output becau…
Comment: i need help mouse prostata single cell data
by
h.mon
32k
Why can't you download MCA data? Did you see the HCL DGE Data download [link][1]?
[1]: https://figshare.com/articles/dataset/HCL_DGE_Da…
Comment: How to interpret min-hash values in phylogeny
by
h.mon
32k
There is no simple answer, and it boils down to understanding the biology (genome evolution), the analysis methods, and making meaningful i…
Comment: Using np to target subsampling
by
h.mon
32k
Add digital normalization to the comparison, you got me curious.
Also, do not forget, the metrics you are reporting are useful, but aren't…
Comment: Low no_Feature value after using STAR for alignment
by
yanyanwu
•
0
My bad, just revised and updated my previous comments. Yes, bacteria generally don't have introns. But as u can see in my previous comments…
Comment: Low no_Feature value after using STAR for alignment
by
swbarnes2
9.9k
Do you expect your organism to have transcripts with exons and introns? Bacteria generally don't. The IGV looks a little weird, generall…
Answer: Extract reads mapped within chosen intronic region from BAM file (no junctions)
by
Pierre Lindenbaum
135k
I quickly wrote something: http://lindenb.github.io/jvarkit/Biostar9469733.html
this tool looks at the cigar string and check if there an…
Comment: Creating Interactive Volcano Plots with R and Plot.ly
by
Kevin Blighe
73k
The error implies that there is no column called 'Fold' in your input data object.
If you still have issues, please try *EnhancedVolcano* …
Answer: Using np to target subsampling
by
andrew
▴
10
In case anyone thinks it's interesting, I tried the nonpareil targeted subsampling on 5 sets of read pairs, and compared it with the origin…
Answer: Merge STAR Log.final.out files together
by
Malcolm.Cook
★
1.2k
STAR comes with a script that [merges Log\.final\.out files from multiple runs into one table](https://github.com/alexdobin/STAR/blob/maste…
Comment: LD matrix in PLINK
by
chrchang523
8.0k
If you want a *square* matrix with the SNPs in `snp_list.txt`, you can replace `--ld-snp-list` with `--extract`.
However, if you want a re…
Comment: QC metrics for each dataset in Seurat for scRNA-seq
by
K.T
•
0
This was quite helpful. I was wondering does 2500 feature counts equate to genes expressed by a cell. And if so, I thought the maximum numb…
Comment: how to obtain annotation file from Genbank file
by
wes
▴
50
Thanks!
May I know how to edit one of the script below using chloroplast genome of [Garcinia mangostana][1] ?
header = """track name=vi…
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