bowtie2

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--al-conc not writing, and -S output flag not being passed correctly?

1

Hello, I am trying to keep reads which align to my reference genome in an output fastq. I have already performed these steps on another computer with the previous build...

bktorrevillas

Unmapped reads

1

Hi, I'm trying to run Bowtie2 on paired-end ATAC-Seq data. Is there any way to write the unmapped reads into the output BAM file with both mates kept? My understanding...

czfoo

cmake build ignores CMAKE_INSTALL_PREFIX

7

As of 2.4.1 the cmake build is ignoring CMAKE_INSTALL_PREFIX. ``` pversion=2.4.1 TOPDIR=/usr/common/modules/el8/x86_64/software/bowtie/${pversion}-CentOS-vanilla wget https://github.com/BenLangmead/bowtie2/archive/v${pversion}.tar.gz gunzip -c v${pversion}.tar.gz | tar -xf - /bin/rm v${pversion}.tar.gz ln -s bowtie2-${pversion} bowtie2 cd bowtie2 mkdir...

mathog

Dear, I am using bowtie2 and SPADES for the de novo assembly of avian influenza viruses of variable concentrations (sequenced with Illumina MiSeq). Avian influenza genome consists of 8 separate...

LauraVP1994

In paired end mode, bowtie2 sometimes reports a mate alignment that does not meet the validity scoring threshold

2

bowtie2 is reporting some alignments that do not meet the scoring threshold in paired-end mode. We see this in two manifestations: 1. bowtie2 reports a concordant pair alignment where the...

barrierbank

bowtie2 not mapping 100% identical reads under very specific circumstances

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Hi, I'm using bowtie2 2.3.5.1 to identify (and remove) contaminating reads. This has worked well so far; however, a very small amount of reads fail to map to the reference...

jborner

--version not showing a bowtie2 version

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Dear Whom It May Concern, I ran into this problem while using humann3 from biobakery. It was not recognizing bowtie2 because it seems it could not recognize a version https://forum.biobakery.org/t/humann-3-cannot-call-bowtie2-version/576/5....

djbradshaw2

Similarity/Dissimilarity between two aligned sequences using bowtie 2

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I have aligned 2 sequences (say **a** & **b**) using bowtie 2. Using the alignment, how I can get a quantity of similarity/dissimilarity between **a** & **b**? I have heard...

mahi045

'-a' does not return all alignments even with -D 100 -R 5

1

Hi I have an amplicons library with a few hundred targets that are similar, I expect no gaps, and for simplicity I expect no mismatches (so I penalize). I use...

shim699

A question of "Randomness in Bowtie 2" in the manual

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> The pseudo-random number generator is re-initialized for every read, and the seed used to initialize it is a function of the **read name**, nucleotide string, quality string, and the...

seahurt