User: gtasource

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gtasource60
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Posts by gtasource

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Comment: C: How to check the pattern in a specific file present in which other files in a di
... 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 8 months ago by gtasource60
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Comment: C: How to check the pattern in a specific file present in which other files in a di
... 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 8 months ago by gtasource60
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Answer: A: How to check the pattern in a specific file present in which other files in a di
... 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 8 months ago by gtasource60
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Online Sequence Alignment of COVID-19 and Other Viruses (H1N1, Ebola, ect)
... 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? ...
forum sequence written 8 months ago by gtasource60
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How to Find Cell Type From Marker Genes (SC-RNA-Seq)
... 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 ...
sc-rna-seq written 13 months ago by gtasource60 • updated 13 months ago by Kevin Blighe69k
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How to Choose PCs from a HeatMap
... 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 ...
rna seq single cell written 13 months ago by gtasource60 • updated 13 months ago by Kevin Blighe69k
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Masked ENV_NT for Kraken2
... 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! ...
kraken2 written 15 months ago by gtasource60
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Comment: C: Removing Unmapped Reads from SAM File (SAMTools)
... 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 15 months ago by gtasource60
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Removing Unmapped Reads from SAM File (SAMTools)
... 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? ...
samtools written 15 months ago by gtasource60 • updated 15 months ago by swbarnes29.4k
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Metagenomic Assembly and Kraken2
... 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 ...
kraken2 metagenomic written 15 months ago by gtasource60 • updated 15 months ago by h.mon32k

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Scholar 8 months ago, created an answer that has been accepted. For A: How to check the pattern in a specific file present in which other files in a di
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to check the pattern in a specific file present in which other files in a di
Popular Question 13 months ago, created a question with more than 1,000 views. For Introns from Exons of GTF File
Popular Question 17 months ago, created a question with more than 1,000 views. For logCPM to RPKM
Popular Question 17 months ago, created a question with more than 1,000 views. For Bedtools Coverage Read Counts
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