Please does anyone have a way to resolve the multiple alignment from bowtie2 to produce alignments with only the best alignment score? A hit at …

Hi all, I would like to get the number of reads mapped to contigs that are greater than 1000 bp in my assembly. I ran …

Hello everyone! I am in need of using Bowtie2 to find all possible alignments for a set of reads (each 23bp long) to the human …

Hi all! My reads contain several ambiguous (N) bases at both the 5'-end and 3'-end (specifically 5 and 4 bases respectively). So it looks like …

This has been bugging me for awhile now. I know there are multiple mapping reads in my alignments, but bowtie2 does not assign the 256 …

Hi, I ran an alignment on Bowtie2 and in the output of the SAM file, I understand that there is an AS tag that signifies …

I need to know if there is any read mapping to certain region in an alignment file (.sam). In fact, I have a list of …

I've been having a lot of problems using bowtie in conjunction with eXpress (http://bio.math.berkeley.edu/eXpress/tutorial.html) to align and count RNA-seq reads. I decided to try to …

Every few weeks there's a post here asking how to get 'unique' alignments from bowtie2 output - there's a question from me in the archive, …

<p>Hi all, I'm new to bioinformatics and I've a question about bowtie2. I know that bowtie2 reports read that map to the reference genome, but …