User: gtasource
gtasource • 60
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Posts by gtasource
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... Thanks for the catch!! It should still be
intersect[[i]]$Genes
Because that's the name of the column in the intersect data frame. ...
written 4 months ago by
gtasource • 60
0
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2
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... Play around with the code and see if you can come up with a solution yourself. We aren't here to hand-spoon solutions (and to be fair, the codes that have been provided are more than enough for you to figure the rest out.) ...
written 4 months ago by
gtasource • 60
3
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... If you don't mind using R, this will do the trick. Install the packages first:
install.packages("tidyverse")
install.packages("magrittr")
And then run the code:
library(tidyverse)
library(magrittr)
genes <- list.files(pattern = "file\\d*.csv")
genes.read <- lap ...
written 4 months ago by
gtasource • 60
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... Besides the Biostar handbook where they go over sequence alignment of different COVID-19 strains, is there an online resource where people have aligned COVID-19 with other viruses that have arisen in the past? ...
written 4 months ago by
gtasource • 60
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1
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1
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... Hey guys,
I know that for a lot of people, looking at the market genes of a cluster is something that is done manually. Obviously, if you know a lot about the tissue you are dealing with, it’ll be easier to say that these marker genes are indicative of this cell type. But what if you have no idea ...
written 10 months ago by
gtasource • 60
• updated
9 months ago by
Kevin Blighe ♦ 66k
1
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1
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284
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1
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... For any sort of single cell program, a big step is picking the amount of principal components for downstream analysis. However, the one approach that does not make sense is when people say to use heat maps. For starters, what exactly are we looking for when we analyze our heatmaps for, let’s say 5 ...
written 10 months ago by
gtasource • 60
• updated
10 months ago by
Kevin Blighe ♦ 66k
0
votes
0
answers
222
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... I'm looking to use the custom env_nt database for Kraken2, but it's taking forever to mask the file. Does anybody have an already masked env_nt database file I can download directly to speed up this process? Thanks! ...
written 11 months ago by
gtasource • 60
0
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1
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235
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1
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... Just to clarify, the * in the chromosome signifies unmapped reads? So, in the above command, since I am extracting unmapped reads into a separate file, that file should have mostly reads with * in the chr field. ...
written 11 months ago by
gtasource • 60
0
votes
1
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... I know, this question is everywhere. But I have yet to see somebody use the same samotols command as myself, and I wanted to double-check.
samtools view -S -f 4 aligned.sam > unmapped.sam
Yay?
...
3
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1
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... Hi all,
We have some metagenomic shotgunning data that we assembled into contigs using SOAPdenovo. Now, we wanted to feed these contigs into Kraken2. However, I've looked over some literature, and it seems like most people feed the raw reads into Kraken2. Is there any advantage using contigs? O ...
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