User: wangdp123

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wangdp123200
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Oxford
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Posts by wangdp123

<prev • 73 results • page 1 of 8 • next >
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featurecounts output changes the underscores in the sample name into dots
... Hi there, In the latest version Rsubread package, I run the featurecounts analysis on a few samples but the output has changed the underscores in the sample names into dots, which is very inconvenient. For example, the original bam file name: **sample_1.bam** the new sample name: **sample.1.bam* ...
featurecounts written 1 day ago by wangdp123200 • updated 1 day ago by Gordon Smyth1.4k
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Paired-end metagenomics data for MEGAN analysis
... Hi there, I am very interested in using the software such as Diamond and MEGAN to process the metagenomics data. The data is not 16S RNA but all genes. I wonder if you could help me with the following three questions: 1) I have paired-end data, is it a good practice to merge them together before ...
metagenomics megan written 9 weeks ago by wangdp123200 • updated 9 weeks ago by h.mon29k
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Deal with the time-course RNA-Seq datasets
... Hi there, I have a set of time-course RNA-seq datasets. The experiment design is as follows: 1. For each condition, there are 3 replicates. 2. In total, there are 5 time points: T0; T1; T2; T3; T4. I notice that there is a tutorial from this website (http://master.bioconductor.org/packag ...
time-course rna-seq written 5 months ago by wangdp123200 • updated 5 months ago by andrew.j.skelton735.9k
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The number of peaks in microRNA-Seq trimmed data
... Hi there, From the adaptor-trimmed single-end microRNA-Seq datasets, I observe that there are three peaks in terms of the read length. > 1) peak 1 at 11bp; > 2) peak 2 at 22bp; > 3) peak 3 at 43bp. The 22bp peak should indicate the enrichment of microRNA species. But how about 11bp ...
rna-seq microrna written 6 months ago by wangdp123200 • updated 6 months ago by jperezboza10
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Comment: C: Which genome fasta file and GTF file to be used in the RNA-Seq analysis
... Thanks for the answer. I have two further questions about this. 1) Should we keep the GTF file and reference FASTA file consistent? For example, if we choose "Genome sequence, primary assembly (GRCh38) - **PRI**" for FASTA file and we have to choose "Comprehensive gene annotation - **PRI**" for GT ...
written 6 months ago by wangdp123200
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Which genome fasta file and GTF file to be used in the RNA-Seq analysis
... Hi there, There are two types of genome fasta files for human species from GENCODE database (https://www.gencodegenes.org/human/): > 1) Genome sequence, primary assembly (GRCh38) - ALL: Nucleotide > sequence of the GRCh38.p12 genome assembly version on all regions, > including reference c ...
rna-seq gencode written 6 months ago by wangdp123200 • updated 6 months ago by Kevin Blighe53k
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Is calcuNormFactors necessary in the calculation of RPKM?
... Hi there, It seems that there are two ways of calculating RPKM values based on rpkm function of edgeR from the output of featurecounts. One uses calcuNormFactors and the other doesn't. I wonder which one is more appropriate for generating RPKM values from RNA-Seq analysis? Why? 1) x <- D ...
rpkm rna-seq edger written 6 months ago by wangdp123200 • updated 6 months ago by ATpoint28k
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Comment: C: Primer sequences in fastq files from 16s rRNA experiment
... Thanks for this comment. Further to this question, after removing the 5'-primers for both R1 and R2 reads from fastq files and assembling the reads from fastq files together, it is seen that the primer-like sequences appear in the 5'-end and 3'-end of the merged contigs, which is because it has seq ...
written 9 months ago by wangdp123200
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GTF file in Ensembl database for RNA-Seq analysis
... Hi there, I am using Ensembl gtf files to carry out RNA-Seq analysis. I am interested in the expression levels of mRNA and long-noncoding RNAs in the data and I find that the gtf files contain not only mRNA and lncRNA but also a variety of non-coding RNAs such as miRNA, snoRNA, rRNA and misc_RNA. ...
gtf rna-seq written 9 months ago by wangdp123200 • updated 9 months ago by Benn7.9k
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Primer sequences in fastq files from 16s rRNA experiment
... Hi there, I am working on the analysis of 16s RNA datasets using mothur toolkit. In the fastq files, the illumina adaptor overhang sequences have been eliminated but primer sequences are still present. 1. Would you like to provide some advice on whether the primer sequences should be removed from ...
16s rrna mothur written 9 months ago by wangdp123200 • updated 9 months ago by gb1.3k

Latest awards to wangdp123

Great Question 5 months ago, created a question with more than 5,000 views. For The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
Popular Question 5 months ago, created a question with more than 1,000 views. For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question 9 months ago, created a question with more than 1,000 views. For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation

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