User: newbio17

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newbio17240
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Posts by newbio17

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Comment: C: what is the difference between gene regularity network and metabolic network?
... I think looking up central dogma of molecular biology and figure 1 from [this paper][1] will be a good starting point regarding your question about the difference between the two networks. I'm not sure what you mean by a 'general network'. [1]: https://journals.plos.org/ploscompbiol/article/figur ...
written 9 days ago by newbio17240
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Comment: C: testing set for RNA-seq AML
... Realistically, it's going to be tough to find what you need. Since you're working with TCGA, I think you might want to try pan-cancer models first to increase the size of your dataset. Or you can really dig through GEO to find RNA-Seq data and accompanying clinical information in the published manus ...
written 9 days ago by newbio17240
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Comment: C: testing set for RNA-seq AML
... Your TCGA expression data was probably generated using GDC workflow for RNA-Seq. You should be able to generate the dataset on your own by following the workflow. ...
written 10 days ago by newbio17240
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Comment: C: testing set for RNA-seq AML
... Have you tried [GEO][1] or [cBioPortal][2] to see if they have any dataset you could use? [1]: https://www.ncbi.nlm.nih.gov/geo/ [2]: https://www.cbioportal.org/ ...
written 12 days ago by newbio17240
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Comment: C: RNASeq data: STAR low alignment score
... If you want another method of checking for rRNA to double check, you can try `split_bam.py` from [RSeQC][1] package. You can also try `read_distribution.py` from the same package to check for potential gDNA contamination. [1]: http://rseqc.sourceforge.net ...
written 12 days ago by newbio17240
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Comment: C: heatmap in R
... Have you tried dropping the rows with NAs as p-values with `na.omit(res)` before applying the filter? ...
written 17 days ago by newbio17240
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Comment: C: WES or WGS
... Generally, as others have already stated, it's a trade-off between cost and the regions sequenced. Also, the enrichment process for WES can lead to non-uniform coverage which results in regions with very high or very low coverage. This may result in missed variant calls in regions with low coverage. ...
written 18 days ago by newbio17240
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Answer: A: convert GATK germline CNV .vcf output to .seg/.cns format to plot
... There is a way to do this in their documentation [here][1] under section "Visualize gCNV results in IGV and compare to truth set calls". It's a three step process right below the IGV figures. Once you have the `.seg` files, you can use `cnvkit.py import-seg` to convert them into `.cns` files. [ ...
written 19 days ago by newbio17240
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Comment: C: Small RNA data analysis
... There is a study looking at different aligners for performing miRNA alignment which could be of use for you (table 3 discusses parameters used): [Evaluation of microRNA alignment techniques][1] [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931105/ ...
written 20 days ago by newbio17240
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Comment: C: mapping of drug names of excel sheet and tsv files
... If it's something that needs to be done only once, you could just export 2nd sheet of the Excel document and perform mapping afterwards. ...
written 20 days ago by newbio17240

Latest awards to newbio17

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Regions & Covered BED files for Agilent SureSelect All Exons v2
Scholar 6 weeks ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf
Supporter 7 weeks ago, voted at least 25 times.
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Appending sequence decoys and virus sequences to reference genome (GRCh38)
Popular Question 5 months ago, created a question with more than 1,000 views. For Orientation of reads in .fastq files from RNA-Seq
Popular Question 6 months ago, created a question with more than 1,000 views. For Orientation of reads in .fastq files from RNA-Seq
Scholar 8 months ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf
Scholar 8 months ago, created an answer that has been accepted. For A: Looking for dbSNP b144 version vcf

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