User: wangdp123
wangdp123 • 230
- Reputation:
- 230
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- Oxford
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- 1 week, 3 days ago
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Posts by wangdp123
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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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... 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 25 days ago by
wangdp123 • 230
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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 ...
0
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1
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142
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1
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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 ...
0
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1
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142
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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
wangdp123 • 230
0
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1
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142
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1
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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
wangdp123 • 230
3
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1
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... 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 ...
written 7 weeks ago by
wangdp123 • 230
• updated
7 weeks ago by
Gordon Smyth • 1.5k
3
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2
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132
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... 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* ...
written 9 weeks ago by
wangdp123 • 230
• updated
9 weeks ago by
Gordon Smyth • 1.5k
1
vote
2
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240
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2
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... 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 ...
written 4 months ago by
wangdp123 • 230
• updated
6 weeks ago by
onestop_data • 200
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