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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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Warnings In Bowtie Mapping

Hello, I am trying to use bowtie on small synthetic data for short read mapping. My command is ./bowtie -p 8 -t -S hg19 -1 synthetic_sample1.fq -2 synthetic_sample2.fq > bowtie.sam. The alignment...

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Trimming 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...

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Bfast 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...

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How 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...

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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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How 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...

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Forum: Attempting to understand pair end sequencing, mainly illumina

Hi I am currently attempted to understand how pair end sequencing works. I understand the basics that it sequences from both ends and if there is an overlapping region they can be joined to create...

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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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Bwa 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...

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Amos 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...

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Coverage 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...

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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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How 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...

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Difference Between "Mate Pair" And "Pair-End"

Just as the title , I can't tell the difference between those two conception. :) waiting for your help.

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Forum: 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...

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Tool Recommendation Wanted For Cleaning Fasta/Fastq Files To Remove Unpaired...

Hi Everyone, I've been digging around the web trying to find a tool that would allow me to clean-up my paired-end Illumina data before mapping. My pipeline thus far has been to:1) FASTQC - my R1 file...

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Filter 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 >...

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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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Download 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...

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