How 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 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 ArticleHow 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...
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 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 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
View ArticleAmos 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...
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 ArticleUsing Paired End And Orphaned Singles For De Novo Assembly
I have been using FastX to process reads prior to de novo assembly and mapping. What I have discovered and few have pointed out is the FastX will delete reads leaving reads unpaired which changes the...
View ArticlePair End Sequencing Problem
Dear all,I have a quick question on pair end sequencing. I used to work with Illumina without the pair end reads and I have dificulties to understand how the pair end reads work.In the "old" system you...
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 ArticleBwa 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...
View ArticleIn Paired-End Data, If One Read Of The Pair Is Unmapped, Is That Pair...
Hello everyone, I have a simple question about generic paired-end Illumina data. If one read of a pair is unmapped, does this automatically mean that the pair is improper and is (un)flagged in a SAM...
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 ArticleIdentifying mutations from Paired-End Sequencing data
Hello! I'm trying to get mutations from paired-end sequenced reads aligned with BWA using SamTools. Coverage is about 16,000. Generally it works fine, but in one fragment (TGGGC) i see that in reads...
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 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 ArticleDoes Every Read In Paired-End Sam File Have The 0X0001 Flag?
Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?...
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Trinity Question
Hi， I 'd like to use Trinity to analyze my strand-specific pair-end sequencing data (dUTP) and I am very confused about how to choose the argument. I got two reads files, _1.fa and _2.fa. For...
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...
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