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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...

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How 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...

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take 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...

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Wgsim 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....

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Is 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...

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samtools 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...

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Is 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...

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why 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...

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How 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...

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basic 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

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Counting 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...

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Paired-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...

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Merging 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...

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Paired-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...

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Analyzing 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...

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Does 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,...

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Coverage 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...

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Resampling 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...

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What 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...

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X 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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