Paire-End Alignments And Scripture
Hello, I am slowly getting my hands on Scripture and have stumbled on yet another unclear (at least to me )detail. I have paired-end data and the two pairs are in a sigle TopHat-derived *.bam file. I...
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 ArticleIdentifying mutations from Paired-End Sequencing data
Hello! I'm trying to get mutations from paired-end sequenced reads aligned with BWA using SamTools. Coverage is about 16,000. Generally it works fine, but in one fragment (TGGGC) i see that in reads...
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 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 ArticleIs There Any Advantage Of Paired End Sequencing For Chip-Seq?
Hi,I hope that some of you may have a recommendation regarding the use of paired-end sequencing over single-end for ChIP-seq. In principle we expect only a minor improvement of using paired-end...
View ArticleOrientation in paired-end sequencing?
I am new to bioinformatics and currently learning how to use Bowtie 2. As written in the manual: A pair that aligns with the expected relative mate orientation and with the expected range of distances...
View ArticleTophat - 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 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 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 Articlejoin non-overlapping paired-end reads
I have a batch of illumina paired end reads with a shorter than anticipated reverse sequence for a ~550bp amplicon.The joining tools which I have used before (i.e. USEARCH, ea-utils) talk about merging...
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 ArticleHow To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
Hi all, I am trying to check if a FASTQ is single or paired end. From wikipedia I saw that default format has to be like this:@HWUSI-EAS100R:6:73:941:1973#0/1but in my case the sequence id is...
View ArticleHow To Convert A Soapsnp Output File To Soap, Sam Or Bam Formats
Hello,I would like to know if there is any tool to convert SOAPsnp to SOAP? Once it is converted to SOAP, I can convert it to SAM using Soap2Sam from reseqtools. Hopefully using reseqtools is not that...
View ArticleBest Cnv Software?
Hello,I know there are many reviews out there, but I can't seem to find exactly what I like.I found this software called mrCaNaVaR, and it's great since it has it's own aligner which is supposed to be...
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 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 ArticleTool: Trim Adapters Of Paired-End Reads (Fastq)
Trimming adapter sequences of paired-end experiments is sometimes a problem. If you clip the mates in two steps, it migh happen that you loose one mate, but not the corresponding one, resulting in two...
View ArticleForum: Mapping Of Ngs Short Reads
This is a simple explanation of how the mapping of short reads works !http://www.youtube.com/watch?v=1ZyoI-4ObSA&feature=related see the first 16 min ! It helped me a lot to understand the basic...
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...
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