Hi again! Thank you for being so prompt with the answers. I appreciate it. Question, if my read length is 101 bp, should I use bowtie2 instead of bowtie? I have been using bowtie to map the reads as most of the tutorials use bowtie, however the length of their reads is usually 36. I have been getting good results (I assume, it generates apprx. 31000000 lines) with bowtie, but I was wondering if bowtie2 is the proper program to use and whether the results could be different. Also, for the map with BWA (the one that galaxy has a tutorial on, with the two replicates), there is no built in arabidopsis genome. Does that mean I cannot use it to do the mapping? Thanks again!
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Question: bowtie vs bowtie2
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jenyka_dm • 10 wrote:
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Jennifer Hillman Jackson ♦ 25k wrote:
Hello,
Bowtie2 could be used. The differences are explained in the Bowtie2 release notes.
This genome (there are three builds we support) is not yet indexed for BWA or BWA-MEM (another choice) at Galaxy Main https://usegalaxy.org but we will be adding these in during the next data update. For now, use the Custom Genome function. This is how: https://galaxyproject.org/learn/custom-genomes/
Thanks! Jen, Galaxy team
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