Does Every Read In Paired-End Sam File Have The 0X0001 Flag?
Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?...
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 ArticleWhat Does Requirebothendsmapped From Rsubread Package Means?
Hi,I am using the featureCounts from the Rsubread package. And I am trying to understand what does the requireBothEndsMapped option do. The manual says"logical indicating if both ends from the same...
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 ArticleMerging Illumina Paired End Reads
Dear All,I have fastq a dataset containing forward and reverse sequences obtained through paired end module of Illumina platform. I am trying to merge these paired end reads. I have a query which I...
View ArticleDealing With Read Counts Under Pe And Se Scenarios
Hi, I am unsure how to deal with this case to go about analysing RNA-seq data. Suppose that you have a control and treatment setup with 4 biological replicates each. However, two in control and two in...
View ArticleHow To Extract Information From Fastq Pair End Files
dear BioStars users,I would like to extract from my pair-end fastq files information how many times my read is occurring in my fastq file. So output could look - my read (sequence) - how many times I...
View ArticlePicard Matequery Slows Process To A Crawl
I'm looking to iterate through an indexed BAM file using picard and perform various tests on both a read and it's mate. For some I would need the full SAMRecord for the mate so I can't just use the...
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 Article20 Mate Alignment With Gaps To Reference Genome
I'm trying to align a string of twenty 5-mers with gaps of 100 to 400 bp to a reference genome. It's similar to paired-alignment except instead of N=2, N=20. The order of the twenty 5-mers is known. Is...
View ArticleUnderstanding Samtools Flagstat Output
The following is the output of samtools flagstat command on bam file (paired-end) generated after markDuplicate of Picards.7417232 + 0 in total (QC-passed reads + QC-failed reads) 287618 + 0 duplicates...
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 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...
View ArticleEstimating Insert Size From Paired End Data.
Hi,I have paired end data from illumina. To estimate the insert size in silico ( from scratch ), I have aligned the reads as single end reads to the genome ( mouse ). Now I have the two alignment files...
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 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 ArticleHow To Rearrange Paired End Bam File?
Hello all,I have a paired end bam file and I want to use bedtools for them. After merging, the paired end read alignments are not lying next to each other. It is making problems in the bedtools...
View ArticleUsing Paired End And Orphaned Singles For De Novo Assembly
I have been using FastX to process reads prior to de novo assembly and mapping. What I have discovered and few have pointed out is the FastX will delete reads leaving reads unpaired which changes the...
View ArticleAssembly Aligned Paired-End Reads
Hi all,I have a set of mapped paired-end reads and I would like to assemble the ones that overlap respecting the pairing information.This means assemblying only pairs when the 2 first mates overlap and...
View ArticleHg19 Strand Information Of Sam Output.
Hi all,I've got Paired-End Illumina data mapped against the Human Hg19. When viewing the SAM output, how can I check if a pair mapped against the forward Hg19 genome sequence or against the reverse...
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