bowtie2

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SwAligner::alignGatherEE16 trying to alloc 32TB in expandCopyExact

1

I have absolutely no knowledge in this field, but I tired to help someone who is getting a crash when trying to sequence some data. (Linux X86_64) I could tell...

tuxsoft

bowtie-inspect --wrapper basic-0 lambda_virus.1.bt2

1

Hi I am using Bowtie2 version 2.2.5. I am facing mentioned error while inspecting. bowtie-inspect --wrapper basic-0 lambda_virus.1.bt2. My index files are in the same directory. Does anybody know the...

Wasim100

reads aligned concordantly exactly 1 time

2

Dear all, How can I get the reads aligned concordantly exactly 1 time reported by bowtie2? For example, 72235868 reads; of these: 72235868 (100.00%) were paired; of these: 1504901 (2.08%)...

lissur

SAMFormatException in aligned reads

1

Hello all, I am analysing some ChIPseq data. I aligned the reads with Bowtie2 (using the pre-indexed human genome from Bowtie2 website, File: GRCh38 no-alt, analysis set), the command I...

GiuliaGuiducci

bowtie2 index generates only tmp files

1

I am running ```bowtie2-build ref.fna ref --threads 12 --large-index``` with no error message. However, the command generates only temporary output files and no .rev files. Log: ``` Settings: Output files:...

mmpust

Conda install uses version 2.2.5

2

When I created a new conda environment and ran `conda install bowtie2 -c bioconda` it installed version 2.2.5. I am interested in using the multithreading with the index builder, which...

ryandikdan

Alignment of pairs missing individuals

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I am using bowtie2 to find reads or read pairs that are chimeric, aligning partly to a virus and partly to human. I initially align the data to the virus,...

jakewendt

Installing Bowtie2

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Hi Would greatly appreciate assistance in installing bowtie2 utilizing my terminal on MacOSX. I am unfamiliar with coding on the terminal Thank you! Best Tom

tlarocca282

I'm hoping to fork bowtie2 and make some changes to how mismatches are tolerated in upfront read alignment and potentially seeding. I am trying to align a set of relatively...

bmorledge-hampton19

Hi, when I use bowtie2 to perform CUT&Tag alignment. I set -X 700 and filter the reads whose mapq700 in bam file. I wonder why I get this result?

NJU-Bio-Info