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A better way to map sequencing reads using existing read mapping tool
Our group just published a paper on improving sequencing read mapping. We achieved this without inventing a new read alignment tool. The key is to customize... -
Why Tophat calls as unique reads which clearly map to many locations?
Hello,
I am starting to use Tophat (latest build) to map RNA seq reads (human) and I am trying to understand some of the results which I am seeing.... -
Postdoc position, INRIA Lille-Nord Europe, Lille/France
We propose to combine a sensitive read mapping process with a multiple reference set, with an assembly approach taking into account paired-end information... -
Read results explanation?
Read 1 Read 2
Lane Aligned Error Aligned Error
1 0.94% 0.19% 0.92% 0.42%
2 0.96% 0.19% 0.94% 0.38%... -
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?... -
Data Analysis Suggestion for a Newbie?
Hi all, I am a newbie in Bioinformatics. I've got data for paired-end DNA sequencing on Illumina platform and I am wondering if anyone is kind enough... -
Illumina single-ended reads
Hi All,
I would like to learn RNA-seq analysis, but unsure of where to get "Illumina
single-ended reads" to get me started.... -
Aligning paired end read files that have different numbers of reads after trimming
Hi all,
Basically, I'm wondering if tophat2 (calling bowtie2) can align paired reads from two different files that don't have the same...Last edited by d1antho; 01-19-2013, 12:50 PM. Reason: The initial title wasnt specific enough to the problem -
bowtie - reads aligned does not match reported alignments
Hi,
A bowtie question of output interpretation,
CMD:
bowtie -p 16 -a --best --strata -q -S --sam-nohead -q... -
BowTie Accuracy
I am experimenting with BowTie v 1 for various length reads (75 to 200 bp). Now, my task is to find it's throughput and accuracy. But, I can't understand... -
Illumina produced Read Length
I am comparing BowTie vs BWA for various read lengths. Now, before one year ago Illumina produced read lengths are typically 36, 75 or 100 bps which they... -
sequence alignment
Hi all,
I want to align some read data in fasta format. i use bowtie short read aligner. but before i align them, i need a refrence sequence. im...Last edited by biouser; 08-14-2012, 11:46 AM. -
summarizeOverlaps vs countOverlaps
Dear All,
I am getting completely different results for the count of mapped reads on transcript features using the countOverlaps... -
Best aligner for 20% mismatched?
I have 101 base reads and expect up to 20 mismatches to reference. My reads are not pairs. I have tried bwa bwasw -a 1 -b 1 -T 60 but it only aligns...
