User: wangdp123

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wangdp123110
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Posts by wangdp123

<prev • 38 results • page 1 of 4 • next >
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The m6A-Seq analysis
... 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 ...
chip-seq m6a-seq written 2 days ago by wangdp123110
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What is the difference between single-cell RNA-Seq and typical RNA-Seq in terms of data analysis procedure
... 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 ...
single-cell rna-seq written 3 days ago by wangdp123110 • updated 2 days ago by Devon Ryan81k
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samtools and I/O redirection
... 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 ...
samtools written 7 days ago by wangdp123110
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The errors reported when running snakemake file with log function
... 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 ...
snakemake written 10 days ago by wangdp123110 • updated 9 days ago by Devon Ryan81k
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The logging file for snakemake
... 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 ...
log snakemake written 23 days ago by wangdp123110
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How to normalize the bam files for RNA-Seq samples for visualization
... 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 ...
normalization rna-seq visualize written 9 weeks ago by wangdp123110 • updated 9 weeks ago by trausch1.0k
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The inclusion or exclusion of NR transcripts in RefSeq gene annotation in the RNA-Seq analysis
... 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 ...
refseq rna-seq written 12 weeks ago by wangdp123110 • updated 11 weeks ago by h.mon15k
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The estimate index of codon bias
... 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 ...
codon bias written 3 months ago by wangdp123110
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Cluster genes based on their codon usage
... 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 ...
cluster gene codon usage written 3 months ago by wangdp123110
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Process the VCF files for a huge number of samples
... 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 ...
vcf indel exome-seq snp written 3 months ago by wangdp123110

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