User: mmrcksn

gravatar for mmrcksn
mmrcksn50
Reputation:
50
Status:
Trusted
Location:
Last seen:
2 years, 2 months ago
Joined:
2 years, 10 months ago
Email:
m******@gmail.com

Posts by mmrcksn

<prev • 9 results • page 1 of 1 • next >
2
votes
1
answer
1.3k
views
1
answer
Duplicate reads in RNA-seq
... Hi everyone, I have some paired end RNA-seq samples that have high levels of duplication (some as high as only 6% remaining after de-duplication). I think it was due to low concentration of input RNA (~1ng), and smaller subset of genes being expressed (because the RNA is from a specific cell type ...
reads duplicate picard rna-seq written 2.4 years ago by mmrcksn50 • updated 2.4 years ago by igor7.1k
0
votes
0
answers
1.0k
views
0
answers
Comment: C: Could high duplication be from ribosomal RNA in RNA-seq samples?
... Thanks for your reply! I am pretty new to all this so I just wanted to make sure. ...
written 2.4 years ago by mmrcksn50
2
votes
0
answers
1.0k
views
0
answers
Could high duplication be from ribosomal RNA in RNA-seq samples?
... Hello, I have some paired-end RNA-seq data. My samples were pretty low concentration (~1ng) total RNA from an isolated cell type. For library prep, we did a poly-A capture to select mRNA. The FASTQC reports show pretty bad duplication (some are as bad as only 2% remaining after deduplication). ...
rrna sequencing rna-seq duplication written 2.4 years ago by mmrcksn50 • updated 11 months ago by Biostar ♦♦ 20
2
votes
0
answers
1.3k
views
0
answers
How to make a barplot with error bars of counts from one gene between 2 conditions from DESeq2 data
... I'm very new to R, so this seemingly simple task is proving difficult for me. I want to make a barplot of the counts for one specific gene between two conditions from my gene expression dataset. Here's what I have so far: Generating the DESeq dataset: ` dds <- DESeqDataSetFromHTSeqCount(sampleT ...
R ggplot rna-seq graph deseq written 2.5 years ago by mmrcksn50
1
vote
3
answers
1.8k
views
3
answers
Comment: C: Loop tophat to align multiple RNA-seq files
... Thanks for the suggestion! Still get the same error though. ...
written 2.6 years ago by mmrcksn50
0
votes
3
answers
1.8k
views
3
answers
Comment: C: Loop tophat to align multiple RNA-seq files
... Sure, here's an example: C-CD-15_S14_R1_001.fastq C-CD-15_S14_R2_001.fastq ...
written 2.6 years ago by mmrcksn50
1
vote
3
answers
1.8k
views
3
answers
Comment: C: Loop tophat to align multiple RNA-seq files
... Thanks for the suggestion. I just tried that and it is returning what it should. ...
written 2.6 years ago by mmrcksn50
11
votes
3
answers
1.8k
views
3
answers
Loop tophat to align multiple RNA-seq files
... Hello, I'm a beginner! trying to use a loop to align multiple paired-end RNA-seq samples with tophat. Here's what I have that isn't working (basically using this https://www.biostars.org/p/98222/ a little bit modified): for i in $(ls *.fastq | rev | cut -c 13- | rev | uniq) do toph ...
tophat alignment loop rna-seq written 2.6 years ago by mmrcksn50 • updated 2.6 years ago by dr_bantz80
0
votes
2
answers
1.1k
views
2
answers
How to figure out adapter sequence for Illumina reads?
... I have some paired-end sequencing reads, 300 bp long. The adapter content is too high for both runs according to FASTQC. However, the only overrepresented sequences that show up in FASTQC are polyA and polyT. Why would the adapter sequence not show up as an overrepresented sequence? And is there an ...
adapter sequence rna-seq written 2.9 years ago by mmrcksn50 • updated 2.9 years ago by genomax59k

Latest awards to mmrcksn

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1000 users visited in the last hour