User: wangdp123
wangdp123 • 200
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Posts by wangdp123
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3
votes
2
answers
93
views
2
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... 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* ...
written 1 day ago by
wangdp123 • 200
• updated
1 day ago by
Gordon Smyth • 1.4k
0
votes
0
answers
113
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0
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... 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 ...
0
votes
1
answer
227
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1
answer
... 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 ...
written 5 months ago by
wangdp123 • 200
• updated
5 months ago by
andrew.j.skelton73 ♦ 5.9k
0
votes
1
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146
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1
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... 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 ...
written 6 months ago by
wangdp123 • 200
• updated
6 months ago by
jperezboza • 10
0
votes
1
answer
400
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1
answers
... 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
wangdp123 • 200
7
votes
1
answer
400
views
5 follow
1
answer
... 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 ...
written 6 months ago by
wangdp123 • 200
• updated
6 months ago by
Kevin Blighe ♦ 53k
1
vote
1
answer
292
views
1
answer
... 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 ...
0
votes
1
answer
338
views
1
answers
... 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
wangdp123 • 200
1
vote
1
answer
273
views
1
answer
... 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.
...
5
votes
1
answer
338
views
1
answer
... 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 ...
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