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!
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