Dna 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 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 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 ArticleJoining Paired-End Illumina Raw Reads
I recently have amplicons sequenced (Illumina PE250) to investigate microbial community. I want to know what quality detection, and what kind of trims of raw reads by what programs should be performed...
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 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 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 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 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 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 ArticleWhy Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are...
I have a sample's data, using illumina 's Piar End sequencing technology.RE19E2T40PA_L1_I040.pairPrimer_1.fastq (Read1) RE19E2T40PA_L1_I040.pairPrimer_2.fastq (Read2) I have aligned both Read1 and...
View ArticleAligning Reads To Specific Chromosome Using Bwa
Hello Everyone,I have whole genome illumina paired end reads and I want to align my reads to specific chromosome (chr 21) using BWA. I was thinking of aligning the entire reads to fasta file of the...
View ArticleResampling Fastq Sequences Without Replacement
Hello, I want to extract a random sample (without replacement) of 7.5 million fastq sequences from illumina sequencing data that contains about 30 million sequences each in of the reads. I want to...
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 ArticleMapping Applications On Hadoop Cluster
Hello,I would like to know if there are any new mapping applications for paired end data designed to work on hadoop cluster. The mapping applications that i know are CloudBurst (single ended), Crossbow...
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 ArticleHow To Interpret Crossbow Data
Hello,May I know how to interpret Crossbow output. Is there any chance of building a SAM or BAM file from Crossbow output. I am looking into genome mapping. I know there are many tools available for...
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 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 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...
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