bowtie2
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BenLangmead
A fast and sensitive gapped read aligner
Hi, I found some bugs in the latest version of bowtie2. 1. A crash can happen when I use the following command with the attached file. The file is an...
I've encountered what I think is a bug in bowtie2 (v2.3.5.1), or at least if it's a feature it's not behaving as I'd expect given the documentation. I'm running bowtie2...
Hi! I am trying to align 12 FASTQ files, but I run into an issue where bowtie2 takes these files as extra parameters If I run the alignment with just...
When enabling Travis s390x on my forked repository removing the commented lines, bowie2 `make simple-test` is failed. Here is [the Travis log](https://travis-ci.org/github/junaruga/bowtie2/jobs/673807050#L497). ``` ... ./bowtie2 --quiet -a --reads-per-batch 7 -x...
Link to download FASTA files matching the GRCh38 bowtie2 indexes, currently returns an error: ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj.fa.gz In fact, the whole FTP server seems out of commission at the moment. Is this...
Hi Bowtie2 developers, I have long insert (10kb) pair-end reads and tried to map them to a genome assembly using default settings. This did not work well. How to adjust...
Hi, I am trying to build an index. but I got the following error: `exceeded integer bounds, remove adjacent SNPs, use haplotypes, or switch to a large index (--large-index).` but...
I've just subjected my poor laptop to an hour's intensive crunching with bowtie2 only to realise that the number of reads in the paired-end files was not the same. Could...
I am trying to align paired-end reads from Drosophila melanogaster to a reference DM6 genome. I have run into the error several times when I ran the following command: /Volumes/LAB/bowtie2-2.3.4.3/bowtie2...
Hi! The current Bowtie2's behaviour is to report a single random alignment if a read/read pair maps equally well to multiple references. For some applications, it would be interesting to...
