bowtie2
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BenLangmead
A fast and sensitive gapped read aligner
With 101bp length illumina sequences, Recorded in Paper's Supplementary Table1, the Peak memory footprint is 3.24 GB, both unpaired and paired. But in practical test using v2.4.2, the Peak memory...
I found another place where `--sam-append-comment` is not writing correctly to the output. This time when using the `--passthrough` option. The output is as follows: ``` A00739:517:HM2C7DSX2:4:1339:6551:28213 16 chr4 118734914...
Hello, I have been working on the metatranscriptomics (2x150 bp), and I want to align the adapter-free and high-quality sequences to the Silva rRNA database, to remove the mapped rRNA...
Both `bowtie2-build --help` and `bowtie2-build -h` prints default ``` Bowtie 2 version 2.4.4 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea) Usage: bowtie2-build [options]* reference_in comma-separated list of files with ref sequences bt2_index_base...
Saw ASCII character 0 but expected 33-based Phred qual. terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 13 (PIPE) what should I do ? thanks!
Hi, I'm getting the issue below -- I've tried to use both the latest version and version 2.3.4.1, which I read on other forums should have resolved this issue. Please...
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...
Hello, I downloaded the mm10 index from Bowtie2 website and ran make_mm10.sh Everything seems to run fine until the end when it just says "failed to build and index" Building...
Hi, I'm trying to align some uBam files using Bowtie2 v2.2.4 with the following commands ``` bowtie2 -b sample_L2.unaligned.bam --preserve-tags --fast-local -x /references/Hsapiens/hg38/bowtie2/hg38 -p 4 bowtie2-align-s -b sample_L2.unaligned.bam --preserve-tags --fast-local...
I'm using bowtie2 (v 2.4.2) with paired-end reads with the the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700 When I look at the distribution...
