bowtie2

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I am using bowtie2 to align some reads against a consensus sequence for young L1s and the alignments are used to predict new insertions. The consensus sequence is relatively short...

esdartez

--dpad --gbar

2

Hi, I'm reading the manual I don't know what's going on here, but if there's a problem, how can I solve it myself? Can you explain? Or provide relevant literature,...

zznx

--no-mixed --no-discordant

1

Hi, ``` --no-discordant --no-mixed --no-mixed --no-discordant ``` I want to know which parameters are used in what kind of analysis scenarios. Thanks

zznx

bowtie2-build only generate .3.bt2 and .4.bt2 two files

1

Hi everyone, I met a problem when using bowtie2 build to generate index for my reference database that it only generate .3.bt2 and .4.bt2 two files instead of six files,...

cyundi

Thank you for developing wonderful tool. I read the paper (https://www.nature.com/articles/s41467-021-22720-0) using bowtie2 for ATAC-seq read alignment, and find the question about pre-alignments. Does anyone know how to use pre-alignments?...

h20gg702