Can't find Bowtie version1 in the tool boxes

Can anyone tell me how to find “Map with Bowtie for Illumina” from the tools? I searched “Bowtie” in the tool search, I only got “Bowtie2” and no “Map with Bowtie for Illumina”. However according to what I learned, I need use Bowtie version1 since my chip-seq sequence are short than 50bp and single ended.

Hi @Sherry

Bowtie version 1 has been deprecated by the original tool authors.

Alternatives include: Bowtie2, HISAT2, BWA and minimap2

Maybe test out mapping with several tools and compare what works best for your specific data?


Thank you @jennaj for the help. I will try all of them then.


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