User: pradyumna Jayaram
pradyumna Jayaram • 170
- Reputation:
- 170
- Status:
- Trusted
- Location:
- Manipal, School Of Life Sciences
- Last seen:
- 2 weeks, 6 days ago
- Joined:
- 3 years, 8 months ago
- Email:
- p**********@learner.manipal.edu
Posts by pradyumna Jayaram
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Comment:
C: How to run EXCAVATOR2?
... Even I didn't run any R script myself, those scripts are run by perl wrapper, there are some R scripts in the folder. If you are getting the exact same error then change the value. or else update your R version and check back. It would be helpful if you provide the error message you are getting. ...
written 27 days ago by
pradyumna Jayaram • 170
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... No we didnot try any pileup based method, Please suggest what tools can be used for that(samtools mpileup?). We got ~400x coverage for the samples. ...
written 11 weeks ago by
pradyumna Jayaram • 170
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... We tried to call variant using nanopolish but we need to specify the ploidy information, which is where we are stuck. can we give ploidy information as 1?
When we give ploidy as 1 we got a warning saying
Number of variants in span (62) would exceed max-haplotypes. Variants may be missed. Consi ...
written 11 weeks ago by
pradyumna Jayaram • 170
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... great!
Thank you very much. ...
written 5 months ago by
pradyumna Jayaram • 170
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... Can we compare 3 normal with 300 tumor sample? CESC in TCGA has only 3 normal samples. ...
written 5 months ago by
pradyumna Jayaram • 170
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... It seems like the data is for single sample. the same read count is available for multiple samples and can be merged. I'm Guessing to go with DESeq2 or EdgeR for differential analysis. can limma be used for same? which one would be more effitient in identifying differential expression? ...
written 5 months ago by
pradyumna Jayaram • 170
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... @kevin Yes it is miRNA-seq data from TCGA ...
written 5 months ago by
pradyumna Jayaram • 170
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... Hi,
@skjobs1234 did you find an appropriate answer for your query? Even I'm performing the similar analysis.
...
written 5 months ago by
pradyumna Jayaram • 170
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... I have 10 samples and 1 pooled Control sample will it work good? ...
written 16 months ago by
pradyumna Jayaram • 170
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... Hello Everyone,
Can anyone suggest the tool to detection of copy number variation from the data obtained from Ampliseq exome sequencing Iontorrent proton platform. I have tried different tools like Excavator2, cnvkit, FreeC, Ionreporter. Each tool gives different region of CNV from the data. ...
written 16 months ago by
pradyumna Jayaram • 170
• updated
16 months ago by
erwan.scaon • 640
Latest awards to pradyumna Jayaram
Popular Question
10 months ago,
created a question with more than 1,000 views.
For How to extract a region from a reference sequence which does not align with a given query read?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How to extract a region from a reference sequence which does not align with a given query read?
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