bowtie2

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Can someone push 2.5.1 release to bioconda please?

1

Can someone please push the 2.5.1 release to bioconda - assuming it's production-ready! thanx :-)

russellsmithies

bowtie2-build and --threads

4

Hi I just cloned the code from here and compiled under ubuntu 22.04 and also from conda, and both ways it was just bailing out after Using parameters --bmax 59599219...

raygozag

Does the newest version of bowtie2 not have a pre-built SRA enabled version?

3

Building bowtie2-3.5 with the SRA fetch builtin is not working for me, and it seems after 3.5.1 the pre-built binary stopped supporting this functionality

jmrussell

Output only unmapped read of pair to --un-mates/conc, when only one maps

1

Hi I was wondering if it was possible to write only the unmapped read of a read pair to the unmapped output. It would be fine for me if the...

ohickl

I am using bowtie2 for metagenomics analysis, and my index always contains many sequences. When I using "-k 100", the output 100 aliment may only contains result of 30 or...

seahurt

--nodc option not working

1

Hello, I am familiarizing with the bowtie2-build, trying different options. However, --nodc option is not giving me output, stats are as follow: Settings: Output files: "nodc.*.bt2" Line rate: 6 (line...

tekitekitekiteki

## Background I am new to the world of bioinformatics, and am trying to interpret the output of `bowtie2-align`: ```txt 57 0 16 14186687 255 23M * 0 0 AGAGAGTTAAGGGCTTACAGCGG...

jamesbraza

Alignment performance decreases with higher `-p` option value

5

I am using Bismark to conduct alignment of methylation NGS data. The alignment engine used is bowtie2. There are 2 options in Bismark related to multi-core processing: `-parallel` determines how...

LawrenceLiu023

Hello I am working with some CAMI dataset consisting in simulated reads from a mock community. Bowtie2 does not recognize the reads as valid fastq, even if they are and...

jtamames

Error, fewer reads in file specified with -1 than in file specified with -2

4

Hi, I have paired end ATACseq data. bowtie2 -p 110 --local --no-mixed --no-discordant --very-sensitive -I 25 -X 5000 -x "$bt2/GRCh38" -1 "$read1" -2 "$read2" -S "${name}.sam" 2> "${name}.bw.map.stat" Error, fewer...

abulislam