Aligning 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 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 Articletake a subset of a fastq paired-end sample
Hi,I have two paired-end fastq compressed files coming from HiSeq RNA-SEq experiment, ie., pair.1.fastq.gz and pair.2.fastq.gz.The files are very large so I wanted to just take a few million/thousand...
View ArticleWgsim mutations in output after setting everything to 0
I was just wondering, is there any useful information on wgsim? Tutorial? Anything? I have been stuck with it for the last 2 weeks. I'm really not sure how to use it. I need it for a project of mine....
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 Articlesamtools count paired-end reads
Hi,I used tophat to align paired-end reads from an rna-seq experiment and I obtained an accepted_hits.bam alignment file.Using the accepted_hits.bam I'd like to count the number of properly aligned...
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 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 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 Articlebasic paired-end sam questions
I can't seem to find answers to 2 very basic questions.For a paired-end sam, is there a separate sam line for mate1's and mate2's? If so, how do find the mate of a given sam line?Thanks
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 ArticlePaired-end protocol for microRNAseq
In another post, a guy wanted to know how to analyze paired-end data and use them to predict microRNAs.I never heard about a paired-end protocol for miRNAseq and would be interested in some more...
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 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 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 ArticleDoes order within read pairs in interleaved files matter?
I have now ended up with interleaved paired-end read files where the order of reads is not the same throughout the file, ie. sometimes the forward read is first, sometimes the reverse read is first,...
View ArticleCoverage for pair-end RNA-Seq, extend reads or not?
HI, allI 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 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 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 ArticleX and Y chromsome crossover position alignments
How do I find the genotypes on the X chromosome which match the Y SNPs listed in raw data from 23andMe, Ancestry or FTDNA
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