Similar posts • Search »

• Reads q-index nucleotides one per one
  Hello, I am working with fastq file from cDNA. A complete transcriptome was sequenced using Illu...
• Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score does not seem to do the trick in my case)
  Hello, I am pretty new to bioinformatics and to this forum, and would very much appreciate any ...
• Bowtie --Very-Sensitive Option
  hiii all, i have a paired end data with each read having 100nt i am using ./bowtie2 -q -D 20 -R ...
• Difference between marking duplicates and filtering BAM on phred score
  Hey! I am working with whole genome sequencing data of bacterial samples and have done an Illumi...
• R: How to test for trend of risk scores
  I have some case/control data like so (many more rows) ID score phenotype 1 0...
• EBSeq explained to a biologist
  **Disclaimer 1: I also posted this in the [EBSeq google group][1], but it does not seem to attrac...
• Quality trimming for denovo assembly
  Is quality trimming of raw reads (Illumina Paired End; 2 X 300 bp) for de novo assembly using SPA...
• Calculating trait disparity between sister species
  I have a phylogeny and 3-D morphometric data. I want to calculate trait disparity between sister ...
• Samtools Mpileup Snp Calling Improperly Paired Reads
  I'm doing samtools mpileup snp calling but samtools is not including reads that are improperly pa...
• Which Data Format Should I Use To Display My Own Data In Igv
  For each one hundred base of the chromosome 1 of human genome, I get a score, as follows: chr...
• Weird Outputs With Dynamictrim And Lengthsort On Custom Settings
  Hi guys, I am using Illumnia Hiseq sequence reads 100bp paired end raw data.I have been toying w...
• Using a gene signature to stratify patient samples
  Hi, I have mRNA expression data and through machine learning analysis I identified a gene signat...
• How to find Standard Error (SE) values when not provided in GWAS summary stats?
  Hi everyone! I'm trying to do a fixed effect meta-analysis on a couple of GWASes based on p-valu...
• samtools view -q 30 filter out most of my reads
  I used the samtools view to filter my alined reads using STAR. But when I set the q-30. most of m...
• Transcriptomic Coordinate Bam To Genomic Coordinate Bam
  Hi, I want to ask how to convert the transcriptomic coordinate bam file to genomic coordinate bam...
• How To Calculate Genotype Likelihood Using Quality Scores For Reads
  After google search and reading some articles, I still have no idea how to calculate genotype lik...
• Comparing Quality Of Read 1 And Read2 Of Illumina Pe
  Hello: I have been asked to compare the quality of read one and read 2 of a illumina PE sequencin...
• Low-coverage whole-genome sequencing (LC-WGS) or ultra low-pass WGS analysis
  I am new to the genome analysis and want to analyse ultra low-pass WGS data for copy number varia...
• Hypergeometric test of gene list overlap
  I have several lists of genes, say A, B, C. I want to test if the overlap between A and B; A and ...