User: c_u

gravatar for c_u
c_u290
Reputation:
290
Status:
Trusted
Location:
United States
Last seen:
1 week, 4 days ago
Joined:
5 years, 11 months ago
Email:
c***************@gmail.com

Posts by c_u

<prev • 131 results • page 1 of 14 • next >
0
votes
2
answers
8.2k
views
2
answers
Comment: C: python: find percentage of match between two sequences
... This is a great answer. Could you mention the import command that needs to go at the beginning of this code? I think we would need to import Biopython and Needle? ...
written 5 months ago by c_u290
3
votes
2
answers
181
views
2
answers
Code/Tool to locally do sequence alignment
... Hi, I have a sequence (A). And I have a set of hundreds of other sequences; I want to test the sequence similarity of each of these hundreds of sequences to A. Then I will select the ones that are highly similar. I know there are many online tools, like [Emboss Needle](https://www.ebi.ac.uk/Tools/p ...
alignment sequencing written 5 months ago by c_u290 • updated 5 months ago by wljlinksly50
0
votes
1
answer
3.2k
views
1
answers
Comment: C: How to run local BLAST (Standalone NCBI BLAST+) with Python?
... What does the `subprocess` function do exactly? I looked up the docs, but couldnt figure out. Why wouldnt using BLAST from Biopython be a good idea? ...
written 6 months ago by c_u290
1
vote
2
answers
525
views
2
answers
Comment: C: Should I normalize read counts if I want to run plotPCA?
... Thanks a lot Kevin! That was SUPER helpful ...
written 8 months ago by c_u290
0
votes
2
answers
525
views
2
answers
Comment: C: Should I normalize read counts if I want to run plotPCA?
... Thanks a lot Kevin for the answers at this strange hour on a Sunday! I ran the first code, this time specifying the Readlength as part of the design, but the PCA plot was basically the same - https://imgur.com/3LwzYc8 I ran the second code, which separately removes the batch effect, the result - ht ...
written 9 months ago by c_u290
0
votes
2
answers
525
views
2
answers
Comment: C: Should I normalize read counts if I want to run plotPCA?
... Hi Delaney, thank you for your answer. From this PCA analysis I am hoping to find bad samples that may have gotten contaminated, and I think I do see three of them that are clustered far away. My concern is that I was not expecting clusters for the 2 batches, and wanted to know if I am seeing them b ...
written 9 months ago by c_u290
0
votes
2
answers
525
views
2
answers
Comment: C: Should I normalize read counts if I want to run plotPCA?
... Thanks Kevin! I have provided my code now. I haven't mentioned the info as to which samples are 50bp and which 75bp anywhere in the code. I know which files are which based on filename, and that's how I identified the clusters in the PCA plot. My main doubt is if I should somehow separately normaliz ...
written 9 months ago by c_u290
14
votes
2
answers
525
views
7 follow
2
answers
Should I normalize read counts if I want to run plotPCA?
... Hi, I am trying to do PCA analysis for my samples for initial quality control. I have 2 different sets of samples - one were sequenced 50bp and other was sequenced 75bp (both of them have disease and control cases). To do the PCA on those samples, I ran DEseq2 on them (which necessarily requires non ...
rna-seq written 9 months ago by c_u290
0
votes
2
answers
502
views
2
answers
Comment: C: Can I use DESeq2 for non-coding RNA?
... Thanks for asking. I haven't done it yet. I think one brute force method would be to look at the Human GTF and based on the annotation, make a list of RNA genes, and then find their counts using featurecounts. Is there a simpler way? ...
written 11 months ago by c_u290
0
votes
1
answer
4.5k
views
1
answers
Comment: C: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da
... hey, so what method did you use for DE analysis for lncRNA? ...
written 11 months ago by c_u290

Latest awards to c_u

Good Question 3 months ago, asked a question that was upvoted at least 5 times. For Difference between abundance and counts in RNA-Seq
Popular Question 3 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 3 months ago, created a question with more than 1,000 views. For Do I need to merge bai files also, while merging bam files
Popular Question 3 months ago, created a question with more than 1,000 views. For Finding RNA sequences for a list of genes
Popular Question 3 months ago, created a question with more than 1,000 views. For Where to find a list of rat protein coding genes?
Student 3 months ago, asked a question with at least 3 up-votes. For Difference between abundance and counts in RNA-Seq
Appreciated 4 months ago, created a post with more than 5 votes. For Difference between abundance and counts in RNA-Seq
Popular Question 4 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 7 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 7 months ago, created a question with more than 1,000 views. For Where to find a list of rat protein coding genes?
Scholar 11 months ago, created an answer that has been accepted. For A: Rename samples for plotting using plotPCA
Popular Question 11 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Centurion 13 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 15 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 16 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 16 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 20 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 21 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 23 months ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Voter 24 months ago, voted more than 100 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Program to find genes up/down-regulated by a given gene
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Doing GSEA analysis on a set of genes
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Extracting 5'UTR and 3'UTR bed files from gtf file
Student 2.4 years ago, asked a question with at least 3 up-votes. For Low mapped percentage. How to know if data is junk?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2536 users visited in the last hour
_