Eric Boyden
Eric Boyden
I would actually prefer that `1.0` be treated as a `float` (returning all reads) rather than an `int`, whereas `1` would return a single read. I'd even suggest enforcing this...
According to the manual: ``` As of Bowtie2 v2.4.0, individual preset values can be overridden by providing the specific options e.g. the configured seed length of 20 in the [--very-senitive]...
Hi, Using Bowtie2 `2.4.4` or `bug-fixes` I found that certain output bams break certain downstream tools like fgbio `ClipBam` and Picard `ValidateSamFile`. I traced the problem back to how Bowtie2...
Bowtie2 (2.4.4) outputs the `@HD` line in the header as follows: `@HD VN:1.0 SO:unsorted` Many downstream tools e.g. `fgbio` require query-grouped / name-collated reads but rely on the `@HD` header...
Hi, it would be great if Bowtie 2 could move fastq read header comments to sam tags, similar to the "-C" function of BWA MEM. Although Bowtie 2 supports alignment...
When ClipBam clips one read in a pair to length 0, it properly sets that read's `0x4` "read unmapped" bitflag, and sets the remaining aligned read's `0x8` "mate unmapped" bitflag....
I already raised an issue with Picard, which is similarly affected, and Bowtie2, which is the root cause of the problem. https://github.com/broadinstitute/picard/issues/1764 https://github.com/BenLangmead/bowtie2/issues/365 Briefly, when using a reference with contigs...
Although most tools can read from either a file or stdin and write to either a file or stdout, the manner in which to specify that seems to vary from...
I have looked extensively for a tool that allows parsing a sam read name to extract information and place it in a (customizable) tag, especially for UMI sequences present in...
Would like to be able to pipe non-realigned sam/bam input.