Trimming Adapters For Paired-End Sequences
Hi all,I got illumina paired end fastq files. They told me to trim read 2 at the beginning for ~20 to 30 bp due to the WGA adapters. Can we find the adapters by looking in to the quality? Which tool is...
View ArticleHow To Assemble Genome Generated With Bac Clones?
I have 2 fastq files from illimina with reads length 250b. Sequences from one file obtained by sequencing from "right" and from "left" in another. This is paired end sequencing. As it is whole genome...
View ArticleShould I merge bacterial RNA-seq paired-end data?
Hi,I have bacterial RNA-seq data from paired-end reads (2x75). I'm interested in sense/antisense differential expression.I would like to know if makes sense to merge R1 and R2 into one read (if...
View ArticleBWA MEM mate pair rescue
Greetings,Can someone spell out what this option means? I have several guesses, but would rather ask than guess. -P In the paired-end mode, perform SW to rescue missing hits only but do not try...
View ArticleCounting reads for gene in bacterial genomes
Hi,I'm analyzing paired-end expression libraries of E. coli and wanted to get some advise about how to count the number of reads for each gene. After mapping the reads to the genome I use htseq-count...
View ArticleDifference Between "Mate Pair" And "Pair-End"
Just as the title , I can't tell the difference between those two conception. :) waiting for your help.
View ArticleAligning Paired-End Reads In Single-End Mode
Hello,I have a question on how to align paired-end reads.In cases of very large fastq files, which make aligners like TopHat crash in a server with limited memory in RAM, I have seen people align one...
View ArticleWarnings In Bowtie Mapping
Hello, I am trying to use bowtie on small synthetic data for short read mapping. My command is ./bowtie -p 8 -t -S hg19 -1 synthetic_sample1.fq -2 synthetic_sample2.fq > bowtie.sam. The alignment...
View ArticleHow To Read Maq Paired-End Alignemnt Data Using Bioconductor Packages
Hi all I have maq paired-end alignment files that I want to read into R. I have tried to browse several packages and they all seem to depend on ShortRead package of bioconductor which does not...
View ArticleSamtools Mpileup And Overlapping Paired-End Reads
I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious about how samtools handles pair mates whose read mappings overlap. With regard to the simple example...
View ArticleBest way to map paired-end, uniquely mapped reads with Bowtie2?
This has come up before, but I have never been satisfied with, or completly understood, the answers. My issue is how can Bowtie2 be used to map uniquely mapping paired-end reads (Illumina) to a genome...
View ArticleDna Sequencing Using Abyss-Pe Of Paired End Reads
Hello! I've got to run abyss-pe on 2 files I've got and find the best parameters (k and so on) that would create the best contig coverage (sorry if I'm messing things up, I'm a programmer that had a...
View ArticlePaired-End Protocol For Micrornaseq
In another post, a guy wanted to know how to analyze paired-end data and use them to predict microRNAs.I never heard about a paired-end protocol for miRNAseq and would be interested in some more...
View ArticleHow To Determine If Library Is Strand-Specific
Hello all, this might be a very basic question but I gave it some thought and don't see a satisfactory answer.Let's say I have a FASTQ file from a sequencing experiment. How can one quickly determine...
View ArticlePaired-End Reads Alignment For Variant Calling ?
I'm trying to do variant calling (SNPs, Indels) from exome-sequencing data, and the sequencing was done with paired end reads. I would like to use BWA for mapping/alignment, followed by PiCard and GATK...
View ArticleIs There An Elegant Way To Extract Only The Properly-Paired Reads In A...
I know I should be filtering for the following tags: 99,163,83,147 and I know that samtools would work to get all the pairs. For example:samtools view -F 0x99 -b in.bam I was wondering if there was a...
View ArticlePaired-End Bam Files
Hi,Having two BAM files from NGS data, how can one check if they are the BAM files (left and right) from a paired end mapping of the same sample? Thanks for the help.
View ArticlePaired End Vs Single End Detection
Hi, I am wondering if anyone has a subroutine or function (hopefully in Perl or pseudocode) to detect whether a fastq file is a shuffled paired-end or not. I think I've seen a few different syntaxes on...
View ArticleHow To Count Stand-Specific Paired-End Rna-Seq Reads Overlapping Known...
Dear BiostarsDoes any one how to overlap stand-specific paired-end RNA-Seq reads (BAM) with known protein coding genes (BED) ?I tried the following but I think it is not the correct way ? Would...
View ArticleCounting Reads On Paired-End Strand-Specific Rnaseq Data
Hello everybody, I've a strand-specific paired-end library on which I'd like to perform some standard DGE analysis. However I'm quite unclear about how to go about counting reads. Usually when I have a...
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