User: rmf

gravatar for rmf
rmf270
Reputation:
270
Status:
Trusted
Location:
Last seen:
3 days, 16 hours ago
Joined:
3 years, 3 months ago
Email:
r**********@gmail.com

Posts by rmf

<prev • 98 results • page 1 of 10 • next >
0
votes
0
answers
134
views
0
answers
Comment: C: RNA-Seq identify stably expressed genes
... It's not for normalisation. I actually want to find stably expressed genes. I want to find genes that do not change between tissues. One tissue is easy to get and other is hard. One of the questions is if the easy tissue can be use as a proxy for the hard-to-get tissue. ...
written 26 days ago by rmf270
0
votes
0
answers
134
views
0
answers
Comment: C: RNA-Seq identify stably expressed genes
... So, is it just a matter of running a standard DE analysis and then look for genes with low FC and high p-values? ...
written 26 days ago by rmf270
0
votes
0
answers
134
views
0
answers
Comment: C: RNA-Seq identify stably expressed genes
... Six replicates per tissue. ...
written 26 days ago by rmf270
3
votes
0
answers
134
views
5 follow
0
answers
RNA-Seq identify stably expressed genes
... I normally use Limma for differential gene expression. This time, I am interested in significantly stably expressed genes rather than differentially expressed. So, I am looking for genes that change the least in expression. I am comparing two tissues. And the normal assumption of DGE 'most genes a ...
rna-seq dge written 26 days ago by rmf270
1
vote
2
answers
786
views
2
answers
Comment: C: bwa mem: Passing a variable to read group
... I have added an answer. ...
written 4 weeks ago by rmf270
1
vote
2
answers
786
views
2
answers
Answer: A: bwa mem: Passing a variable to read group
... What worked for me was to read the read group information from the fastq file during the mapping run. My read name in the fastq file looks like this: `@ST-E00274:188:H3JWNCCXY:4:1101:5142:1221 1:N:0:NTTGTA`. The bash file looks like this: #!/bin/bash header=$(zcat $1 | head -n 1) ...
written 4 weeks ago by rmf270
1
vote
1
answer
141
views
1
answer
GATK: .ped vs .fam and missing values
... In the GATK pipeline, it seems like I need to use a *.ped* file for `CalculateGenotypePosteriors` and a *.fam* file for `VariantsToBinaryPed`. What is the difference between *.ped* and *.fam* file? And how do I specify missing parents in both of them? Some options I've seen are zero (`0`), `NO_PAREN ...
variant-calling gatk snp written 7 weeks ago by rmf270 • updated 7 weeks ago by Kevin Blighe19k
0
votes
0
answers
217
views
0
answers
Comment: C: RNASeq: Differential gene expression and qqplot
... Thanks for the input. The sample size is same as before: 24. ...
written 12 weeks ago by rmf270
1
vote
0
answers
217
views
0
answers
RNASeq: Differential gene expression and qqplot
... I ran DGE on my dataset using DESeq2 and Limma. I used the same dataset, similar settings and same GLM model (`~family+condition`). The number of DEGs I get are as below (based on unadjusted p-values <0.05 and BH adjusted q-values <0.05 shown separately): Tool num_degs_pval num_degs_qv ...
deseq2 rna-seq differential gene expression limma written 12 weeks ago by rmf270
4
votes
4
answers
604
views
4
answers
Answer: A: LD-decay in a r2 vs distance(cm) plot
... For LD block length distribution, I ran this on the thinned SNP set. plink --bfile "snp-thin" --blocks --blocks-max-kb 200 --out "snp-thin" This produces snp-thin.blocks.det. Then some R. dfr <- read.delim("snp-thin.blocks.det",sep="",header=T,check.names=F,stringsAsFactors=F) co ...
written 12 weeks ago by rmf270

Latest awards to rmf

Popular Question 11 days ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Centurion 26 days ago, created 100 posts.
Scholar 4 weeks ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: LD-decay in a r2 vs distance(cm) plot
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: LD-decay in a r2 vs distance(cm) plot
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Scholar 12 weeks ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Scholar 12 weeks ago, created an answer that has been accepted. For A: Regenotype vcf using some samples as reference
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: LD-decay in a r2 vs distance(cm) plot
Scholar 3 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Voter 5 months ago, voted more than 100 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 9 months ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 18 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Student 18 months ago, asked a question with at least 3 up-votes. For Consequences of degraded DNA for Sequencing
Scholar 18 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Supporter 2.0 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1051 users visited in the last hour