User: gundalav
gundalav • 210
- Reputation:
- 210
- Status:
- Trusted
- Location:
- Japan
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 4 years, 8 months ago
- Email:
- g*******@gmail.com
about me
Posts by gundalav
<prev
• 43 results •
page 1 of 5 •
next >
0
votes
2
answers
249
views
2
answers
... Thanks. `airway@assays$data$counts` is that normalized or not? If not how can I get the normalized one from S4? ...
written 3 months ago by
gundalav • 210
6
votes
2
answers
249
views
6 follow
2
answers
... I have the following DESeq2 code and the corresponding results
suppressMessages(library(DESeq2))
suppressMessages(library(airway))
data(airway)
airway_se <- airway
airway_dds <- DESeqDataSet(airway_se, design = ~cell + dex)
deseq <- DESeq(airway_dds)
#> ...
0
votes
3
answers
337
views
3
answers
... @b.nota i.e. 100 + 30 = 130 (sum of 7th column of featureCounts output)?? ...
written 5 months ago by
gundalav • 210
0
votes
3
answers
337
views
3
answers
... @b.nota in other words the `totalReads` in the calculation *is not the total assigned reads to the genes*? So I have to directly count from the BAM file? Would prefer to recode cause later need to calculate TPM as well. ...
written 5 months ago by
gundalav • 210
0
votes
3
answers
337
views
3
answers
... I'm interested in processing from featureCounts not htseq. ...
written 5 months ago by
gundalav • 210
3
votes
3
answers
337
views
3
answers
... Lets say the [featureCounts][1] output is this (for convenience only contain 2 genes:
Geneid Chr Start End Strand Length myfile.bam
Xkr4 chr1;chr1;chr1 3214482;3421702;3670552 3216968;3421901;3671498 -;-;- 3634 100
Npbwr1 chr1 5913707 5917398 - 3692 30 ...
written 5 months ago by
gundalav • 210
• updated
5 months ago by
James Ashmore • 1.7k
2
votes
1
answer
242
views
5 follow
1
answer
... In my Amazon EC2 instance I have the following:
ubuntu@ip-333-31-16-230:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 79G 0 79G 0% /dev
tmpfs 16G 8.8M 16G 1% /run
/dev/xvda1 985G 136G 809G 15% /
tmpfs ...
written 5 months ago by
gundalav • 210
• updated
5 months ago by
Devon Ryan ♦ 68k
0
votes
1
answer
235
views
1
answers
... Hi Devon,
Thanks for the reply:
Do you mean this command?
trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 --paired -a CTGTCTCTTATA -a2 CTGTCTCTTATA -o $TRIMGALORE_DIR $READ1 $READ2
...
written 5 months ago by
gundalav • 210
3
votes
1
answer
235
views
5 follow
1
answer
... I have Nextera data, according to the **[document][1]**, the adapter is this:
![enter image description here][2]
My question is what's the right parameter to use for trim_galore?
Does this command suffice?
trim_galore --stringency 5 --dont_gzip --trim1 --length 30 -q 0 --paired --nextera - ...
written 5 months ago by
gundalav • 210
• updated
5 months ago by
Devon Ryan ♦ 68k
0
votes
2
answers
378
views
2
answers
... I tried with your suggestion, doesn't change:
` trim_galore --stringency 5 --dont_gzip --paired --trim1 --length 30 -q 0 -a CTGTCTCTTATACACATCT -o $TRIMGALORE_DIR $READ1 $READ2
` ...
written 5 months ago by
gundalav • 210
Latest awards to gundalav
Epic Question
5 months ago,
created a question with more than 10,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Best Way To Measure Mirna-Seq Abundance
Great Question
10 months ago,
created a question with more than 5,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
10 months ago,
created a question with more than 1,000 views.
For How To Make Cytoscape Export Network In Cluster Format (Non-Sif)
Great Question
2.1 years ago,
created a question with more than 5,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For How To Identify Tissue Specific Genes From Mixed Samples In Microarray Data
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Best Way To Measure Mirna-Seq Abundance
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For How To Embed Ucsc Genome Browser To Web Page
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For How To Remove Noise In Microarray Data?
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Best Practice For Extracting Gene Names From Pubmed Abstracts
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Immune System Specific Gene Ontology Source
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Visualizing Up/Down Regulation Of Genes Based On Fold Change
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Ways To Do Gene Ontology Analysis For Microarray Data
Student
2.1 years ago,
asked a question with at least 3 up-votes.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Student
2.1 years ago,
asked a question with at least 3 up-votes.
For Summarizing Mirna-Seq Data Based On Ucsc Hg19 Alignment Results
Student
2.1 years ago,
asked a question with at least 3 up-votes.
For How To Compute Gene Enrichment P-Value? (Significantly More Than Expected)
Supporter
2.1 years ago,
voted at least 25 times.
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For Best Practice For Extracting Gene Names From Pubmed Abstracts
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For Creating Barplot With Horizontal Marker And Asterisks For Biological Paper
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For Visualizing Up/Down Regulation Of Genes Based On Fold Change
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For Converting Affymetrix (*_At) Mouse Probe Id To Hugo Gene Symbol In R
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For How To Embed Ucsc Genome Browser To Web Page
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For How To Compute Gene Enrichment P-Value? (Significantly More Than Expected)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 471 users visited in the last hour