User: pbigbig

gravatar for pbigbig
pbigbig210
Reputation:
210
Status:
Trusted
Location:
United States
Last seen:
4 months, 1 week ago
Joined:
5 years, 3 months ago
Email:
p***********@gmail.com

Posts by pbigbig

<prev • 99 results • page 1 of 10 • next >
0
votes
1
answer
501
views
1
answers
Comment: C: How do I specify single end Read in CIRCquant?
... Hi, I am sorry for some quick questions about CIRI2: 1. As I understand, CIRI2 can only be used for RNA-seq data that did not undergo polyA enrichment, isn't it? 2. Can I use CIRI2 to construct circRNAs from Small RNA-seq data? Thank you! ...
written 8 months ago by pbigbig210
0
votes
0
answers
263
views
0
answers
Comment: C: miRNA quantification on custom database
... Thank you, I will check it ...
written 14 months ago by pbigbig210
0
votes
0
answers
263
views
0
answers
miRNA quantification on custom database
... Hi everyone, At the moment, I have some small-RNA enriched sequencing data from disease samples, read length is around 20-30 bp, tRNA largely dominated the datasets. Could you please suggest any tool(s) or tutorials for: - Extract and assemble for only miRNA or pre-miRNA - Identify and quantif ...
rna-seq mirna written 14 months ago by pbigbig210
1
vote
2
answers
2.7k
views
2
answers
Comment: C: Get BUSCO gene descriptions
... Oh great! Thank you very much! Although the post was long time ago but I think it still very useful for other de novo genome project. ...
written 14 months ago by pbigbig210
0
votes
1
answer
452
views
1
answers
Comment: C: Calculate scaling factor for RNAseq data
... Yeah, I also thought so. However, you know that it isn't practical to write in a research proposal something for example: "we need to collect 100 brain tissues from these patients with disease and also collect dozen of fresh brain pieces from normal people just to perform RNAseq experiments at the ...
written 16 months ago by pbigbig210
0
votes
1
answer
452
views
1
answers
Comment: C: Calculate scaling factor for RNAseq data
... Yes, because I obtained them from different public databases, so 2 experiment protocols were totally different (however both data are Hiseq Illumina reads) ...
written 16 months ago by pbigbig210
1
vote
1
answer
452
views
1
answer
Calculate scaling factor for RNAseq data
... Hi everyone, I have a RNA-seq expression count matrix of 2 contrast conditions (~10 biological samples per condition), but these conditions are affected by (severe) batch effect from different sequencing experiments. I looked up for some batch-effect removal tools, but they could only fix batch-ef ...
normalization rna-seq written 16 months ago by pbigbig210 • updated 16 months ago by swbarnes28.9k
0
votes
2
answers
11k
views
2
answers
Comment: C: Clustering differences between heatmap.2 and pheatmap
... Sorry to comment on this old post, I also just have noticed this difference when trying to create heatmaps. Do you have any suggestion on which is the better way? Clustering then scaling (like heatmap / heatmap.2) or scaling then clustering (like pheatmap), because the cluster results is quite diffe ...
written 17 months ago by pbigbig210
0
votes
2
answers
1.3k
views
2
answers
Comment: C: which matrix should be used to draw heatmap in RNAseq?
... Thank you very much for your comprehensive answer! So as I understand, graphically in expression matrix, purpose of TPM is for same-column comparison and TMM is for same-row comparison. I think scaling by row will only benefit those who only interested in clusters of highly/lowly expressed genes in ...
written 17 months ago by pbigbig210
7
votes
2
answers
1.3k
views
2
answers
which matrix should be used to draw heatmap in RNAseq?
... Hi everyone, I have some confusion about which type of expression matrices should I use for heatmap visualization of RNAseq data. There are 3 options listed below: (raw count matrix was obtained from featureCounts, TMM cross-sample normalization is performed by edgeR) 1. TMM-normalized raw count ...
rnaseq normalization heatmap written 17 months ago by pbigbig210 • updated 17 months ago by predeus1.4k

Latest awards to pbigbig

Popular Question 10 months ago, created a question with more than 1,000 views. For de novo transcriptome assembly
Popular Question 13 months ago, created a question with more than 1,000 views. For de novo transcriptome assembly
Popular Question 13 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Great Question 14 months ago, created a question with more than 5,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 14 months ago, created a question with more than 1,000 views. For de novo transcriptome assembly
Popular Question 17 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 20 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 20 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 22 months ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 22 months ago, created a question with more than 1,000 views. For Merging BAM file before running GATK or merging vcf output
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Epic Question 2.4 years ago, created a question with more than 10,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Merging assemblies with GAM-NGS
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Extracting ids of a cluster in heatmap
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Extracting ids of a cluster in heatmap
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Scaffolding with SSPACE returned scaffold the same as initial contigs set
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
Great Question 3.7 years ago, created a question with more than 5,000 views. For Run multiple fastq.gz files with FastQC and yield single report?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Jellyfish -C option explanation
Popular Question 3.8 years ago, created a question with more than 1,000 views. For kmergenie can not execute on a file because directory not exist?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For kmergenie can not execute on a file because directory not exist?
Supporter 4.0 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: 1445 users visited in the last hour