User: wangdp123

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wangdp123230
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Oxford
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Posts by wangdp123

<prev • 81 results • page 1 of 9 • next >
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Some questions regarding DESeq2
... 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, ...
deseq2 rna-seq written 10 days ago by wangdp123230 • updated 10 days ago by dsull1.0k
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Forum: A free temporary HPC service for bioinformatic analysis
... 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 ...
hpc forum written 12 days ago by wangdp123230 • updated 12 days ago by h.mon29k
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Perform differential circular RNA expression
... 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 ...
circexplorer2 circrna written 25 days ago by wangdp123230
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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 ...
written 7 weeks ago by wangdp123230 • updated 7 weeks ago by RamRS26k
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Comment: C: The error generated by Rsamtools
... OK. I have run the command line: `samtools quickcheck -vvv sample.bam` The output is below: verbosity set to 3 checking sample.bam opened sample.bam sample.bam is sequence data sample.bam has 1 targets in header sample.bam has good EOF block ...
written 7 weeks ago by wangdp123230 • updated 7 weeks ago by RamRS26k
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Comment: C: The error generated by Rsamtools
... I run the following command line on terminal: samtools quickcheck -v sample.bam The output is empty. ...
written 7 weeks ago by wangdp123230
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Comment: C: The error generated by Rsamtools
... No. I have checked that it is BAM file. I can use asSam() function to convert sample.bam to sample.sam but cannot convert back from sample.sam to sample.bam using asBam() function. ...
written 7 weeks ago by wangdp123230
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The error generated by Rsamtools
... Hi there, I use Rsubread to produce the BAM files and then use Rsamtools to manipulate the BAM files. A few errors were thrown out: 1) > indexBam(files = "sample.bam") Error in FUN(X[[i]], ...) : failed to build index 2) > asSam(file = "sample.bam") > asBa ...
rsubread rsamtools written 7 weeks ago by wangdp123230 • updated 7 weeks ago by Gordon Smyth1.5k
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featurecounts output changes the underscores in the sample name into dots
... Hi there, In the latest version Rsubread package, I run the featurecounts analysis on a few samples but the output has changed the underscores in the sample names into dots, which is very inconvenient. For example, the original bam file name: **sample_1.bam** the new sample name: **sample.1.bam* ...
featurecounts written 9 weeks ago by wangdp123230 • updated 9 weeks ago by Gordon Smyth1.5k
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Paired-end metagenomics data for MEGAN analysis
... Hi there, I am very interested in using the software such as Diamond and MEGAN to process the metagenomics data. The data is not 16S RNA but all genes. I wonder if you could help me with the following three questions: 1) I have paired-end data, is it a good practice to merge them together before ...
metagenomics megan written 4 months ago by wangdp123230 • updated 6 weeks ago by onestop_data200

Latest awards to wangdp123

Great Question 7 weeks ago, created a question with more than 5,000 views. For How to find the hub genes in the gene co-expression network constructed by WGCNA
Popular Question 7 weeks ago, created a question with more than 1,000 views. For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Interproscan get stuck in "90% completed"
Great Question 8 months ago, created a question with more than 5,000 views. For The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
Popular Question 8 months ago, created a question with more than 1,000 views. For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation
Popular Question 11 months ago, created a question with more than 1,000 views. For KGCAK: A K-mer based database for genome-wide phylogeny and complexity evaluation

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