User: gtasource

gravatar for gtasource
gtasource60
Reputation:
60
Status:
Trusted
Location:
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 10 months ago
Email:
g********@mail.com

Posts by gtasource

<prev • 66 results • page 1 of 7 • next >
0
votes
2
answers
190
views
2
answers
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 4 months ago by gtasource60
0
votes
2
answers
190
views
2
answers
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 4 months ago by gtasource60
3
votes
2
answers
190
views
2
answers
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 4 months ago by gtasource60
0
votes
0
answers
99
views
0
answers
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 4 months ago by gtasource60
0
votes
1
answer
595
views
1
answer
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 10 months ago by gtasource60 • updated 9 months ago by Kevin Blighe66k
1
vote
1
answer
284
views
1
answer
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 10 months ago by gtasource60 • updated 10 months ago by Kevin Blighe66k
0
votes
0
answers
222
views
0
answers
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 11 months ago by gtasource60
0
votes
1
answer
235
views
1
answers
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 11 months ago by gtasource60
0
votes
1
answer
235
views
1
answer
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 11 months ago by gtasource60 • updated 11 months ago by swbarnes28.7k
3
votes
1
answer
800
views
1
answer
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 11 months ago by gtasource60 • updated 11 months ago by h.mon31k

Latest awards to gtasource

Scholar 4 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 4 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 9 months ago, created a question with more than 1,000 views. For Introns from Exons of GTF File
Popular Question 13 months ago, created a question with more than 1,000 views. For logCPM to RPKM
Popular Question 13 months ago, created a question with more than 1,000 views. For Bedtools Coverage Read Counts
Popular Question 20 months ago, created a question with more than 1,000 views. For Bedtools Coverage Read Counts
Popular Question 20 months ago, created a question with more than 1,000 views. For edgeR RPKM Values
Popular Question 20 months ago, created a question with more than 1,000 views. For Quick Way to Annotate a Bed File

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 904 users visited in the last hour