Hi all,
I am having some issues interpreting the output from the bamtools stats command. I am working with paired end RNAseq data generated...
19 results in 0.0029 seconds.
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Paired-end RNA-seq: large discrepancy in number of forward versus reverse reads
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Artemis paired end illumina short read mapping won't display any "duplicate" reads
Hi! I'm working with Illumina paired end short reads fastq mapping using Artemis for a course I'm taking. While I'm able to get all SAM/BAM files without... -
Incosistent number of paired end reads (BAM file generated by STAR using RSEM)
I have used RSEM to quantify paired-end RNA-Seq data. The alignment was done
using STAR which was called internally by RSEM, using a reference... -
Coverage plots with inferred fragment sequence from PE reads
Hi!,
I need to make coverage plots/GC bias plots with inferred sequences from Illumina paired-end sequences. Someone here posted that he or she... -
paired end mapping using bowtie
Hi all
I'm really nub to working with bowtie. I have two fq files that contained paired end reads for a child . The files are child1-1.fq and child1-2.fq...Last edited by mansoorhasani; 06-14-2015, 10:55 PM. -
How to filter paired reads that are not mapped?
Hi!,
This should be very easy but it's confusing to me. I would appreciate some help. I have paired end Illumina sequencing. I want to keep only... -
Some chromosomes missing in bwa-output
Hello!
I have fasta-files, resulting from a de novo assembly. When I map pe-reads to these fastas with bwa-mem (default options), it does... -
Make Blastn search with paired end reads
Hi all,
I have a problem to align paired ends read with blastn app to the hg 19.
My reads stored in F3 and F5_P2 files. They are... -
How to extract sequence between paired reads R1 and R2?
Hi all,
I have human paired end Miseq reads 2 by 50 (2x50). My insert size is 400 bp. I mapped the reads using bowtie 2 and I have positons for... -
Stampy - Mapping multiple individuals to genome
Stampy - Mapping multiple individuals to genome
Hi everybody,
I am very very new to this world, so apologize if the following questions...Last edited by vivi7; 03-18-2014, 12:39 AM. -
BWA with multi read files
Hi I have never used BWA before and so was wondering if anyone knows how I can use BWA to map my reads to my reference genome. My data is as follows:... -
Mapping multiple FASTQ data types using BWA?
Greetings!
I plan to do mapping using multiple types of Illumina FASTQ files for the same sample.
I have one set of FASTQs... -
Mapping 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 ones... -
tophat IOError
I get the following error when I run Tophat, when I tested the installation of Tophat and Bowtie I didn't have any issues, any idea what's causing this?... -
Illumina reads failing to map to bacterial genome with Tophat
Hello,
I am working with fastq files generated from an Illumina HISeq 2000. They are 50bp paired end reads. I am trying to align these...
