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User: wangdp123

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wangdp123 • 140
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140
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Oxford
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2 years, 11 months ago
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Posts by wangdp123

<prev • 61 results • page 1 of 7 • next >
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Comment: C: How to collect the phastCons and phyloP data from Ensembl
... Thanks. Any idea about how to get the conservation scores for each gene or exon by making use of the single nucleotide data? I know that the bigwig files contain the conservation score for each nucleotide. Should we use the sum or mean to calculate the scores for single gene or exon? ...
written 7 days ago by wangdp123 • 140
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Comment: C: How to collect the phastCons and phyloP data from Ensembl
... Thanks Emily. Are there any conservation scores for Ensemblgenomes database (http://ensemblgenomes.org/) such as Ensembl Fungi, Ensembl Plants, Ensembl Protists and Ensembl Metazoa? ...
written 7 days ago by wangdp123 • 140
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How to collect the phastCons and phyloP data from Ensembl
... Hi there, Does anybody know if Ensembl/Ensemblgenomes provides the data of sequence conservation scores (e.g., phastCons, phyloP) for each nucleotide of the genomes? If so, where to download the data? Many thanks, Tom ...
ensembl phastcons phylop written 8 days ago by wangdp123 • 140 • updated 7 days ago by Emily_Ensembl ♦ 17k
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STAR+Cufflinks for RNA-Seq analysis
... Hi there, I am using STAR+cufflink combination to handle the unstranded paired-end RNA-Seq datasets. 1. I wonder if there are a set of typical parameters for both STAR and cufflink? For STAR: STAR --runThreadN 1 --runMode alignReads --genomeDir index --readFilesIn sample_r1.fq sample_r2.fq ...
cufflinks star rna-seq written 8 days ago by wangdp123 • 140 • updated 8 days ago by Istvan Albert ♦♦ 79k
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(Closed) TruSeq3-PE primer sequence
... Dear colleague, We are using HiSeq4000 to generate the RNA-Seq reads and can you please tell me which adapter sequence (TruSeq3-PE primer) I could use to trim the paired-end reads? Moreover, it is known that "AGATCGGAAGAGC" can be used for both ends to trim the reads for typical TruSeq adaptors. I ...
adapter trimming rna-seq written 10 weeks ago by wangdp123 • 140
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Comment: A: How to link the assembly accession with the chromosome accession for prokaryotic
... Thanks, Does anybody know why there are some 0 values in the "Genomes" column of the file prok_representative_genomes.txt? For example, "Acetobacter aceti". ...
written 11 weeks ago by wangdp123 • 140
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How to link the assembly accession with the chromosome accession for prokaryotic representative genomes
... Dear colleague, I am working on the analysis of prokaryotic genomes from NCBI genome database. 1. Downloaded a file called prok_representative_genomes.txt from the following file ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prok_representative_genomes.txt After opening the file, we could see ...
ncbi prokaryotic genomes written 11 weeks ago by wangdp123 • 140
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Smart-seq2 single-cell RNA-Seq
... Hi there, The data generated from Smart-seq2 single-cell RNA-Seq protocol seems to have very unbalanced gene expression values. For example, if you did the differential gene expression test, you would find out many genes are only present in one sample group. Is this normal? I wonder if there are s ...
single-cell rna-seq smart-seq2 written 3 months ago by wangdp123 • 140 • updated 3 months ago by kristoffer.vittingseerup • 1.4k
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Comment: C: Can snakemake work with multiple nodes from HPC?
... In this scenario, will snakemake make use of 16 cores (from single node)? At the same time, will the other 9 nodes remain idle? I have taken a look at the manual about --cluster. I feel confused about the usage: snakemake --cluster qsub -j 32 Do this mean we need to run this command within ...
written 3 months ago by wangdp123 • 140
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Comment: C: Use OrthoDB to retrieve the orthologs between human and bacteria
... Thanks for this. I have a quick look at the database but couldn't find the list of genomes that have been included in the database. Am I missing something? ...
written 4 months ago by wangdp123 • 140

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