User: wangdp123

gravatar for wangdp123
wangdp123110
Reputation:
110
Status:
Trusted
Location:
Oxford
Last seen:
4 hours ago
Joined:
2 years, 5 months ago
Email:
w********@gmail.com

Posts by wangdp123

<prev • 44 results • page 1 of 5 • next >
0
votes
1
answer
127
views
1
answers
Comment: C: "Segmentation fault" error from running align function in Rsubread package
... Hi, thanks for this. I have checked the standard error file, which includes the following message: *** caught segfault *** address 0x17a34e074, cause 'memory not mapped' Does this mean anything? ...
written 4 hours ago by wangdp123110
1
vote
1
answer
127
views
1
answer
"Segmentation fault" error from running align function in Rsubread package
... Hi there, When running align function in Rsubread package for one particular RNA-Seq samples, an error message "Segmentation fault" came up and the program stopped at "50% completed". It works for other samples but only doesn't work for this sample. Does anybody know how to tackle this problem? T ...
rsubread rna-seq written 6 days ago by wangdp123110 • updated 5 days ago by i.sudbery2.4k
0
votes
1
answer
230
views
1
answers
Comment: C: What is the difference between single-cell RNA-Seq and typical RNA-Seq in terms
... Hi, thanks for this. I am just handling some SMART-Seq2 single-cell RNA-Seq datasets and it seems that it doesn't use UMI barcodes and its analysis pipeline is quite similar to that of bulk RNA-Seq. Is it true? If not, any differences? Thanks, ...
written 29 days ago by wangdp123110
0
votes
0
answers
123
views
0
answers
Comment: C: The failed compilation of Rsubread
... I have tried updating R to the latest version R-3.5.1 but it still reported the error. I am thinking about if it is caused by the gcc compiler version incompitability? ...
written 6 weeks ago by wangdp123110
0
votes
0
answers
123
views
0
answers
Comment: C: The failed compilation of Rsubread
... Thanks for the reply. I have tried this approach but still got bad luck. > biocLite("Rsubread") BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.0 (2016-05-03). Installing package(s) ‘Rsubread’ trying URL 'https://bioconductor.org/pa ...
written 6 weeks ago by wangdp123110
0
votes
0
answers
123
views
0
answers
The failed compilation of Rsubread
... Hi there, Rsubread package is really a good one but unfortunately, I cannot make it through when trying to install it. Would you like to help me out? The command line is: R CMD INSTALL folder/R_package/Rsubread_1.22.0.tar.gz ----------------------------------------------------------------------- ...
rsubread rna-seq written 6 weeks ago by wangdp123110
0
votes
0
answers
150
views
0
answers
The m6A-Seq analysis
... Hi there, I start to look into the methodology of m6A-Seq data (from cDNA) and surprisingly find that it is quite similar to that of ChIP-Seq (from DNA) data analysis, which includes the main steps: - fastq file processing - mapping against genome - narrow peak (summit) - calling motif identif ...
chip-seq m6a-seq written 8 weeks ago by wangdp123110
3
votes
1
answer
230
views
1
answer
What is the difference between single-cell RNA-Seq and typical RNA-Seq in terms of data analysis procedure
... Hi there, I am working on some single-cell RNA-Seq samples and wondering what the difference between a typical RNA-Seq analysis and single-cell RNA-Seq analysis is? Can we use standard Subread and DESeq2 pipeline to work with the data? Thank you very much, Best wishes, Tom ...
single-cell rna-seq written 9 weeks ago by wangdp123110 • updated 8 weeks ago by Devon Ryan82k
4
votes
1
answer
116
views
1
answer
samtools and I/O redirection
... Hello, I am using 2> and 1> to output the stderr and stdout to two files but when I use samtools to convert test.bam into test.sam, it seems that there is no output in the result file (test.sam). samtools view -h test.bam > test.sam 2> bam2sam.stderr 1> bam2sam.stdout Would y ...
samtools written 9 weeks ago by wangdp123110
0
votes
1
answer
192
views
1
answer
The errors reported when running snakemake file with log function
... Hi there, I am using snakemake to compile a pipeline and encounter an issue as follows: The error reported is: > RuleException in line 284 of pipeline_1.snakemake: Wildcards in input, > params, log or benchmark file of rule fastx_collapser cannot be > determined from output files: 'PIPEL ...
snakemake written 10 weeks ago by wangdp123110 • updated 9 weeks ago by Devon Ryan82k

Latest awards to wangdp123


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 908 users visited in the last hour