Tophat - Understated Number Of Reads In The "Align_Summary.Txt" File
Hi all. I'm working with paired-end rna-seq data to assemble transcriptome of my species of interest. I've just realized that Tophat is understating the number of reads that I actually have and...
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 ArticleSorting Fastq Files After Trimming (Orphans And Pe)
I have a bunch of Illumina PE data that has been run through fastx trimmer and clipper. I am ready to map these reads, but am needing to create 2 files for paired end reads (the left and right hand...
View ArticleNeed help using Shrimp2 on paired end color-space SOLiD data.
Hi, I have SOLiD reads which are paried-end (75bp and 35bp) in .csfasta and .QV.qual format. I would like to use Shrimp2 to align them. So far I have been having trouble using it. I used the following...
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 ArticleHow To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific
I've been provided with more than a billion reads of RNAseq data for a poorly annotated nematode species. They appear to be 2x100 paired-end Illumina reads – I currently know frustratingly little about...
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 ArticleTool Recommendation Wanted For Cleaning Fasta/Fastq Files To Remove Unpaired...
Hi Everyone, I've been digging around the web trying to find a tool that would allow me to clean-up my paired-end Illumina data before mapping. My pipeline thus far has been to:1) FASTQC - my R1 file...
View ArticleIs It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
Hi,I'm wondering if it's OK to use one end of a set of paired-end reads as a set of single reads?I just want to get a single read data set of a sample, but currently there's only paired-end data...
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 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 ArticleWhat Better Way To Get The Paired Reads Aligned Against The Reference Genome?
Hi everybody,I have a group of paired reads sequenced using Solid 4 (50bp each mate). I discovered that reads are contaminated by E.coli. My strategy is to align the reads against the reference genome...
View ArticleCoverage For Pair-End Rna-Seq, Extend Reads Or Not?
HI, all I have a question when computing region coverage of pair-end RNASeq data. As showed by the sketch map, when computing region coverage, whether I should use actually mapped reads or extended...
View ArticlePair End Sequencing Problem
Dear all,I have a quick question on pair end sequencing. I used to work with Illumina without the pair end reads and I have dificulties to understand how the pair end reads work.In the "old" system you...
View ArticleAnalyzing Older Illumina Paired-End Data
Hi all, I've got some reads from mid-2010 that I'd like to re-align. I'm not sure how best to proceed. These are from a Illumina Genome Analyzer IIx. They're 40-bp, paired-end. Here's what the text...
View ArticleForum: Attempting to understand pair end sequencing, mainly illumina
Hi I am currently attempted to understand how pair end sequencing works. I understand the basics that it sequences from both ends and if there is an overlapping region they can be joined to create...
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...
View ArticleChIPseq paired-end bowtie2 concern regarding biological replicates
I am working with ChIP-seq paired-end data where there is concern that one or more of the biological replicates may not be very good, but it is unknown which replicate may have a problem (I suspect...
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 ArticleDoes The Mapping Of A Read'S Pair Affect Its Own Mapping Score In Bwa?
I would like to know more about how BWA treats the mapping score of paired end reads. I am familiar with the process used to assign mapping scores by BWA (thanks to this post). I see that the mapping...
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