User: wangdp123
wangdp123 • 110
- Reputation:
- 110
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- Oxford
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- 2 days, 4 hours ago
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- 2 years, 3 months ago
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Posts by wangdp123
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... Hi there,
I start to look into the methodology of m6A-Seq data (from cDNA) and surprisingly find that it is quite similar to that of ChIP-Seq (from DNA) data analysis, which includes the main steps:
- fastq file processing
- mapping against genome
- narrow peak (summit)
- calling motif identif ...
written 2 days ago by
wangdp123 • 110
3
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... Hi there,
I am working on some single-cell RNA-Seq samples and wondering what the difference between a typical RNA-Seq analysis and single-cell RNA-Seq analysis is? Can we use standard Subread and DESeq2 pipeline to work with the data?
Thank you very much,
Best wishes,
Tom
...
written 3 days ago by
wangdp123 • 110
• updated
2 days ago by
Devon Ryan ♦ 81k
4
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... Hello,
I am using 2> and 1> to output the stderr and stdout to two files but when I use samtools to convert test.bam into test.sam, it seems that there is no output in the result file (test.sam).
samtools view -h test.bam > test.sam 2> bam2sam.stderr 1> bam2sam.stdout
Would y ...
written 7 days ago by
wangdp123 • 110
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... Hi there,
I am using snakemake to compile a pipeline and encounter an issue as follows:
The error reported is:
> RuleException in line 284 of pipeline_1.snakemake: Wildcards in input,
> params, log or benchmark file of rule fastx_collapser cannot be
> determined from output files: 'PIPEL ...
written 10 days ago by
wangdp123 • 110
• updated
9 days ago by
Devon Ryan ♦ 81k
2
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1
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76
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... Hi there,
I am trying to correctly understand how logging system works in snakemake.
In the original tutorial, it states like this:
shell:
"(bwa mem -R '{params.rg}' -t {threads} {input} | "
"samtools view -Sb - > {output}) 2> {log}"
And in other places, I keep ...
written 23 days ago by
wangdp123 • 110
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... Hi there,
I would like to compare the visualizations of bam files from different RNA-Seq samples to get a view of the differences among samples. The software would be golden helix software or IGV viewer.
I am wondering if there is a way to normalize the bam files by taking into account the total r ...
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169
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... Hi there,
The human Refseq gene annotation includes protein-coding genes and non-coding genes and even for the protein-coding genes it is possible to include mRNA (NM_) and non-coding RNAs (NR_) for the same gene at the same time.
For the RNA-Seq analysis, is there a need to remove all the NR_ tra ...
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... Hi there,
Could anybody suggest a number of indexes for measuring the codon bias of each gene in a genome without the expression data?
I know one of the most famous indexes is CAI (Codon adaptation Index) but this will need a prior knowledge of a group of high-expressed genes. But what if the geno ...
written 3 months ago by
wangdp123 • 110
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127
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... Hi there,
I wonder if anybody knows how to cluster genes based on their codon usage and identify the various groups of genes that posses different codon usage patterns, which is analogous to the identification of gene family such as orthoMCL approach.
I know there is one way to do the heatmap but ...
written 3 months ago by
wangdp123 • 110
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193
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... Dear Colleague,
I am processing the VCF files from thousands of samples from exome-sequencing.
I would like to take the three steps as follows:
1. Identify the homozygous SNPs.
2. Identify the minor allele SNPs.
3. identify the SNP/InDel that have deleterious effects on protein function such as n ...
written 3 months ago by
wangdp123 • 110
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