User: wangdp123

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wangdp123140
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Oxford
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Posts by wangdp123

<prev • 57 results • page 1 of 6 • next >
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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 11 days ago by wangdp123140
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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 16 days ago by wangdp123140
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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 18 days ago by wangdp123140
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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 6 weeks ago by wangdp123140 • updated 5 weeks ago by kristoffer.vittingseerup1.0k
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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 8 weeks ago by wangdp123140
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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 8 weeks ago by wangdp123140
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Comment: C: Can snakemake work with multiple nodes from HPC?
... To clarify the process, the batch script test.sh looks like this: > \#Request running time > \#$ -l h_rt=48:00:00 > \#Request the number of nodes > \#$ -l nodes=10 (each node has 16 cores, thus in total 160 cores available from 10 nodes) > \#Request the memory > \#$ -l h_vmem= ...
written 8 weeks ago by wangdp123140
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The difference between heatmap.2 and pheatmap
... Hi there, I have a long standing unresolved question about the difference between heatmap.2 and pheatmap. In general, we could see the clusters produced by pheatmap exhibit a more obvious color pattern (the genes with the similar colors in each row will cluster together first) rather than heatmap. ...
rna-seq heatmap written 8 weeks ago by wangdp123140 • updated 8 weeks ago by Kevin Blighe33k
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Comment: C: Can snakemake work with multiple nodes from HPC?
... What if only put --cores=160 in the snakemake script without using the --cluster argument and then qsub the batch script ? ...
written 8 weeks ago by wangdp123140
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Can snakemake work with multiple nodes from HPC?
... Hi there, I am thinking about how to use snakemake under the HPC system. Can snakemake work with multiple nodes from HPC? For example, I request 8 nodes and each node has 20 cores in the batch script and as a result, I totally request 8*20=160 cores. And then I set the --cores=160. snakemake --c ...
hpc snakemake written 8 weeks ago by wangdp123140

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