User: Tom_L

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Tom_L120
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Posts by Tom_L

<prev • 14 results • page 1 of 2 • next >
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Comment: C: how to extract all the gene in chromosome X in bed file using R package (rtackla
... Why do you want to use a specific package instead of performing some basic filter in Bash/Awk/R ? Is your BED file stored into an object that is package-dependant? ...
written 22 days ago by Tom_L120
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Survival analyses: how to compare multiple groups?
... Hello, I have trouble understanding how do I compare multiple groups in a single survival analysis. When I only have two groups of patients, I simply perform the Kaplan-Meier estimator. How do I deal with supplementary cohorts? If you look at the *colon* data, you will find 3 different cohorts (*r ...
R survival statistics written 23 days ago by Tom_L120
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Answer: A: How to filter/view reads mapped to multiple locations using samtools or pysam
... According to the SAM format specification, I believe you are looking for the NH tag. > NH: Number of reported alignments that contains the query in the current record Page 6: http://chagall.med.cornell.edu/galaxy/references/SAM_BAM_Specification.pdf To filter them: samtools view -h myBAM. ...
written 24 days ago by Tom_L120
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Answer: A: How to calculate the sum of ranks per gene??
... Simplest way (IMO): get the complete miRNA list, get the miRNA rank for each DF column, and sum ranks. R implementation (assuming your miRNA dataframe is "DF"): miRNA=unique(unlist(DF)) sapply(miRNA,function(x) sum(as.numeric(apply(DF,2,function(y) which(y==x))),na.rm=T)) Cheers. ...
written 24 days ago by Tom_L120
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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 4 weeks ago by Tom_L120
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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 6 weeks ago by Tom_L120
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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 6 weeks ago by Tom_L120
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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 8 weeks ago by Tom_L120
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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 8 weeks ago by Tom_L120
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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 9 weeks ago by Tom_L120

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Teacher 4 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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