bowtie2
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BenLangmead
A fast and sensitive gapped read aligner
I think that GitHub's [issue template](https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository) and [pull-request template](https://help.github.com/en/github/building-a-strong-community/creating-a-pull-request-template-for-your-repository) feature guide users how to write and report the issue. Here is the [other project's example](https://github.com/containers/libpod/blob/master/.github/ISSUE_TEMPLATE.md). I have seen the maintainers...
Hi Ben I getting what appears to be an anomalous alignment with bowtie2 (v2.3.4). Consider the following: reference1 M00831:461:000000000-CP4BP:1:2105:10688:18697 99 AGRO_LBA4404_1|NODE_23 996 31 100M = 1213 267 CTCGACTGGCAATGAGAAGTTGCTCGCGCGATAGAACGTCGCGGGGTTTCTCTAAAAACGCGAGGAGAAGATTGAACTCACCTGCCGTAAGTTTCACCTC CCCCCGGGGGGGGGGGGGGGGGGFFGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGGGGGGGGFGGGGFGGG AS:i:200...
Currently Bowtie 2 does not build on [64-bit PowerPC and Power Architecture processors (ppc64/ppc64le)](https://en.wikipedia.org/wiki/Ppc64). There are several portability issues (32/64-bit detection incorrectly using `uname`, and SSE hard-coded in the `Makefile`)....
Hello! After last system updating bowtie2 does not work on any ubuntu machines. How to fix it without system backup? Please help
The read sequence is `ATGCCCAGGTGCTGAAGCCCC`. Bowtie 2 maps this to the guide RNA reference sequence `ATGAACAGGTTCCGCAGCGG` (all of the reference sequences in this analysis are 20 nucleotides long) and gives...
Hi, I am using bowtie 2.3.5.1 and try to get sample and other IDs recorded on the `@RG` line. Unfortunately, it seems bowtie2 does not write TABs as separators on...
Hello, I am trying to extract antibody reads from RNAseq data. Since the antibodies are very diverse, I have made a small database and a a large database, containing verified...
Hi, I used bowtie2-2.2.9, and found a pair of reads aligned discordantly. The flag of read 1 is 97, and read 2 is 145. The offset position of read2 is...
I am mapping paired end data with these parameters: --maxins 5000 --phred33-quals --threads 8 --no-discordant I have a couple of Debian servers to do that. Some of them are AMD...
Hi, I am ultimately trying to use a comparative genomics tool called breseq, but breseq relies on bowtie2. I have posted my issue on the breseq issues page but have...
