User: wangdp123
wangdp123 • 250
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- 1 month 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 4 weeks ago by
wangdp123 • 250
0
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1
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113
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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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1
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140
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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 12 weeks ago by
wangdp123 • 250
• updated
10 weeks ago by
chrchang523 ♦ 7.3k
2
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1
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249
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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 5 months ago by
wangdp123 • 250
0
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1
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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 6 months ago by
wangdp123 • 250
• updated
6 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, ...
6
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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 7 months ago by
wangdp123 • 250
0
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1
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316
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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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