User: wangdp123
wangdp123 • 250
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- 5 months ago
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- 5 years ago
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Posts by wangdp123
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... This is for microRNA analysis. There should be no need for splice aware. ...
written 5 months ago by
wangdp123 • 250
0
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... Hi there,
If the following command line is used to generate the SAM file.
bowtie -q -v 0 -k 10 -S -t
featureCounts program will be used to count the reads by enabling the multi-mapping reads counting:
featureCounts -t miRNA -g Name -O -M -a -o
I wonder how featureCounts with the ...
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... Hi there,
I am attempting to use PLINK2 with its --extract flag to extract the specific set of variants from UK Biobank dataset in *.bgen format. Unfortunately, the variant IDs contained in .bgen file is in rs_id format, which is not unique.
For example, the two different SNPs happening in the sam ...
written 7 months ago by
wangdp123 • 250
• updated
6 months ago by
chrchang523 ♦ 7.7k
2
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1
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... Hi there,
We are planning some proteomics experiments and I have the following two concerns regarding the replicate samples:
1) What are the minimum numbers of biological replicates (from different subjects) and technical replicates (from the same subject but run multiple times) respectively?
2) ...
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... Hi there,
I am looking for some best tools for calculating a variety of codon bias metrics such as RSCU, ENc, CodonO and CAI.
The input data would be a bunch of sequences from numerous genomes.
I have been aware of something like CodonW, GCUA and INCA. However, it seems that those tools have not ...
written 9 months ago by
wangdp123 • 250
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... Hi there,
I wonder if there is a smart way to retrieve the codon tables for all sequences from all contigs/scaffolds/chromosomes for all genomes from Ensembl and EnsemblGenomes databases. I suppose that all sequences from this same chromosome share the same codon table. Consequently, the question m ...
written 10 months ago by
wangdp123 • 250
• updated
10 months ago by
Ben_Ensembl • 1.6k
2
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1
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... Hi there,
I am reading through the manual of DESeq2 package and I have run into two questions about how to use this package properly.
1) In order to perform the variance stabilising transformation, there are two ways of doing this.
i) vsd <- vst(dds, blind=TRUE)
ii) vsd <- vst(dds, ...
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5 follow
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... Hi there,
I am looking for somewhere to run the analysis with run time of 96 hours and high memory of 800G for a short period of time.
Is there any free of charge HPC service for running this?
Any suggestion is welcome.
Many thanks,
Tom
...
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... Hi there,
I am using CIRCexplorer2 to annotate circRNAs from the paired-end RNA-Seq datasets and obtain a file named "circularRNA_known.txt" with the column of number of junction reads.
1) What is the cutoff to defined the expressed circRNAs according to the number of junction reads of each annota ...
written 11 months ago by
wangdp123 • 250
0
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1
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445
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Comment:
C: The error generated by Rsamtools
... @HD VN:1.0 SO:unsorted
@SQ SN:22 LN:50818468
@PG ID:subread PN:subread VN:Rsubread 1.34.7 CL:"subread-align" "-r" "sample.R1.fastq.gz" "-R" "sample.R2.fastq.gz" "-o" "sample.bam" "-i" "index" "--type" "0" "-n" "10" "-m" "3" "-p" "1" "-M" "3" "-T" "1" "-I" "5 ...
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