User: Tom_L

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Tom_L80
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Posts by Tom_L

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How to differentiate SNPs Vs Sequencing error in RNA Seq?
... Recurrence. If multiple reads share the same specific mismatch, it is very unlikely that it is sequencing error. ...
written 2 days ago by Tom_L80
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Answer: A: What is first publication/mention of term RNA-seq
... Actually, there was a paper in 2006 by Bainbridge *et al.* where the authors performed RNA-seq though it wasn't called that way yet. They performed 454 sequencing, obtained thousands of sequences, used BLAST to map them to human transcriptome and determined gene expressions. It sounds like RNA-seq ...
written 18 days ago by Tom_L80
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Answer: A: NGS - Mapping quality of specific regions
... I did that few days ago using *bedtools coverage* (http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html). Give it a BED files (containing your exons) as *-a* and your BAM file as *-b* with and it will tell you how many reads are mapped to each exon (*-counts* argument). ...
written 19 days ago by Tom_L80
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Answer: A: How many paired FASTQ reads to input for alignment if 4 different SRA IDs belong
... > Why are there four different SRA IDs? Are you sure it's the same sample? If so most aligners allow input from multiple files (or pairs of files) I do agree with Asaf, most aligners handle multiple paired-end inputs. Some of my colleagues deal with multiple paired-end FastQ files and they proc ...
written 4 weeks ago by Tom_L80
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Answer: A: why allelic count on forward and reverse strand do not add up to depth in the re
... The first four values of the I16 tags are depths at Q13 threshold, corresponding to 10^(-13/10) base calling error, which is 5% (documentation: http://samtools.sourceforge.net/mpileup.shtml). Would it be possible that 15 is the total depth without taking into account any base calling threshold wher ...
written 4 weeks ago by Tom_L80
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Comment: C: How to perform Fisher's exact test between two gene lists for a particular gene
... If you can summarize your dataframes into two columns "MAP3K1" (containing values "wt" and "mutant") and "LIST" ("list1" and "list2") then you could use *table()* to automatically generate contingency matrices. I don't know how easy this will be since I don't know the architectures of your dataframe ...
written 5 weeks ago by Tom_L80
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Comment: C: How to perform Fisher's exact test between two gene lists for a particular gene
... Are you talking about the FET implemented in the *fisher.text()* function? Can you please post an example so we can understand what kind of data you want to analyze? ...
written 5 weeks ago by Tom_L80
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Answer: A: validating SNPs from NGS Analysis for multiple samples
... My colleagues (biologists) validate variants on both cDNA (to fit RNA-seq experiment at mRNA level) and genomic DNA (to determine if variant is heterozygous or homozygous) with Sanger sequencing. There also is a good reason to do both: you validate the variant with two independent experiments. If y ...
written 5 weeks ago by Tom_L80
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Effects of cohort size on survival estimation
... Hello, I'm currently working on survival analyses using different cohorts. I found a striking evidence of relationship between cohort size and survival difference (the larger cohort size, the better survival differences). This sounds logical to me since a big cohort allows more classification error ...
R written 6 weeks ago by Tom_L80
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Answer: A: How can I integrate gene with PPI network
... You can use the bioconductor package "[STRINGdb][1]", assuming you're a little comfortable using R programming language. Basically, you can obtain your PPI network with 3 commands: string_db=STRINGdb$new(version="10",species=9606,score_threshold=400,input_directory="YOUR_PATH") myDF=string ...
written 3 months ago by Tom_L80

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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How can I integrate gene with PPI network

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