bowtie2
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BenLangmead
A fast and sensitive gapped read aligner
Hello， I'm using bowtie2 to align with chromosomes above 2GB and it fails. Is this because of tool limitations? Is there any solution？ Best wishes！
I am confused by the behavior of the -k and -a options. I am attempting to align a set of short (23-31 bp) reads which may have up to two...
It's not an issue, just a question. I have as an input HiSeq paired end reads, around 500 GB in size (both of them). What size of .sam file should...
Hi, I am using Bowtie2 often, it is a great program. Today, when starting a read mapping run, however, I came across a cryptic error message that took me some...
Hello, I just want to confirm the appropriate alignment mode. The default mode of bowtie2 is end-to-end alignment. Some posts say that if two sequences have approximately the same length...
Not sure if this issue is better placed on the bioconda issue board, but the most recent version of TBB (v2021.1.1) causes a runtime error with the `bowtie2-align-s` binary available...
Hello, just an easy question. What is the optimized read length for bowtie2 to handle? Can bowtie2 handle the reads shorter than 50 bp? For instance, the reads with 30...
Hi, so I've used bowtie2 many times before, but I have now encountered an unexpected problem with the indexing process on the last version (v2.4.5). So I downloaded the GRCm39...
First I am not a very experienced user. But I installed GetOrganelle and it crashes on bowtie2. I tried installing on 2 different macs, but no luck. Any help appreciated....
Hi, #I used old version (2.2.5) for mapping, and I got around 90% overall alignment rate. However, when I used new version, I could only get overall alignment rate less...
