User: Tom_L

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Tom_L150
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Posts by Tom_L

<prev • 20 results • page 1 of 2 • next >
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Answer: A: How to choose a reference genome when there's no genome information in database
... Do not use a genome that is not related to your experiments, Ever. How about: http://www.ensembl.org/Gadus_morhua/Info/Index (click on "*Download DNA sequence*")? ...
written 23 days ago by Tom_L150
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Comment: C: Merging of datasets from same tissue/region
... I don't understand what kind of structure do want to process and obtain. I mean, it seems like your DF is already merged so why sub-setting DF1 with the first 42 columns and DF2 with other columns but a single line? ...
written 26 days ago by Tom_L150
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Comment: C: Merging of datasets from same tissue/region
... To merge dataframes (DF) by row names, use *DF=merge(DF1,DF2,by="row.names")*. Also, you cannot merge multiple DF like this unless you store them into a list. Make a loop and iterate on each DF you want to merge or create a list of DF and use join_all function from plyr package (https://www.rdocumen ...
written 26 days ago by Tom_L150
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Comment: C: Strand specific pair end Illumina sequencing
... R1 is left, R2 is right. ...
written 26 days ago by Tom_L150
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Answer: A: Strand specific pair end Illumina sequencing
... A strand-specific library from illumina sequencing certainly refers to dUTP sequencing. According to the RSeQC documentation, your results confirm that you deal with dUTP sequencing: http://rseqc.sourceforge.net/#infer-experiment-py dUTP sequencing corresponds to the *RF* value in Trinity documenta ...
written 26 days ago by Tom_L150
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Comment: C: Bowtie fails to align reads that appear in the reference sequence
... Interestingly, your non-mapping reads correspond to reference regions including several N's. Have a look at the Bowtie2 "*--n-ceil*" (func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)) and "*--np*" (penalty for non-A/C/G/Ts in read/ref (1)) options. As you said, you replaced ambiguous characte ...
written 26 days ago by Tom_L150
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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 7 weeks ago by Tom_L150
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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 7 weeks ago by Tom_L150
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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 7 weeks ago by Tom_L150
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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 7 weeks ago by Tom_L150

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Teacher 5 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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