Mapping trimmed paired end reads with MapSplice
Hi!I'm trying to map illumina paired end using MapSplice. I used script named sickle to trim the bad quality tails and the output looks like this:Paired end 1@TUPAC_0006:1:1:3062:1473#0/1...
View ArticleFilter paired-end sam file for XT:A:U
Dear all,I have a sam file (BWA output, paired-end reads). I would like to retain only reads which are "properly paired". This I would do by:samtools view -f 0x002 file.sam >...
View ArticleAMOS with paired end data
Hi all, how do I take advantage of paired end data with AMOS? I have a 2x100bp fastq file that I would like to use AMOScmp-shortreads with. I see that when I google for it, there might be a .mates file...
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 Articlebwa sampe segmentation fault
Hi everyone,I'm running bwa in the sampe mode and, after successfully processing >10M reads it fails with a segmentation fault (as follows) on what appears like a set of poorly-alignable reads. Any...
View ArticleDownload large paired-end RNA-Seq and microarray data of the same sample (>...
Hi,I was trying to find if there is any large size paired-end RNA-Seq and microarray data of the same sample, but I wasn't able to find as much data as I wanted.Could somebody please point out where I...
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 Articlepaire-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 ArticleExisting tools for post-processing after aligning paired-end reads with BLAT?
Hi,I'm wondering if there are existing tools that can do post-processing on paired-end reads' BLAT output.More specifically, I'd like the tool to "merge" the alignments from the alignments of each...
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 ArticleTophat 2 - both pairs map concordantly
Hi,I have just run the following command tophat2 --solexa1.3-quals -p 12 -r 80 --max-multihits 1 --no-mixed --no-discordant /home/Turkey/Index/turkeyindex /home/Turkey/WTCHG24920061sequence1.fa...
View ArticleMapping 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 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 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 ArticleSequence Variation Detection for Prokaryotic Genomes
I have resequenced a bacterial genome using SOLiD paired end reads. After looking at SNPs and small Indels, I'm now interested in large Insertions/Deletions (Size of genes and gene clusters).Which...
View Articlebfast match paired end reads - reports half total number of reads
I'm using bfast 0.7.0a and testing on the paired end data present in the bfast user manual (Figure 5.4 in bfast-book.pdf). The format for this fastq file is shown that paired reads should follow...
View Articletrimming 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 ArticleTrim 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 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 ArticleHow to read maq paired-end alignemnt data using bioconductor packages
Hi allI 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 currently...
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