How To Read Maq Paired-End Alignemnt Data Using Bioconductor Packages
Hi all I 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...
View ArticleHow To Count Stand-Specific Paired-End Rna-Seq Reads Overlapping Known...
Dear BiostarsDoes any one how to overlap stand-specific paired-end RNA-Seq reads (BAM) with known protein coding genes (BED) ?I tried the following but I think it is not the correct way ? Would...
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 ArticleHg19 Strand Information Of Sam Output.
Hi all,I've got Paired-End Illumina data mapped against the Human Hg19. When viewing the SAM output, how can I check if a pair mapped against the forward Hg19 genome sequence or against the reverse...
View ArticleForum: 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...
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 ArticleAlign Paired End Reads Using Blast
Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only...
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 ArticleMapping target-enriched reads to a transcriptome reference
Hi all, I have carried out transcriptome sequencing on a plant species and then, from the resulting assembled contigs, have designed capture probes for 970 gene regions. I then carried out...
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 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 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 ArticleHow does the calculated inner-distance between reads change after trimming...
If we had an insert length of 426bp and an adapter size of 65bp, then the length of the central region between two 100bp reads would be 96bp (426bp - 130bp - 100bp - 100bp). So providing the mean...
View ArticleShould We Dump Illumina Pair-End Mapping Results In Sam With Mapq=0, But Good...
hi, everyone! I am working on illumina pair-end sequencingAfter mapping by bwa, I got a pair of reads with MAPQ=0, with both reads mapped to more than one place. But the Template Length is OK, and I...
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 ArticleHigh level of duplicate in one reads of paired-end data
Hi,We are doing some transcriptomic analysis on bovine immune blood cells and we seem's to have some problem with high levels of duplicate in our data. Our library were prepared with the illumina...
View ArticleHow 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...
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 ArticlePaired-End Bam Files
Hi,Having two BAM files from NGS data, how can one check if they are the BAM files (left and right) from a paired end mapping of the same sample? Thanks for the help.
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....
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