Question: bowtie vs bowtie2
0
gravatar for jenyka_dm
5 months ago by
jenyka_dm10
jenyka_dm10 wrote:

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!

bwa-mem bwa bowtie mapping bowtie2 • 421 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by jenyka_dm10
1
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k 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

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for jenyka_dm
5 months ago by
jenyka_dm10
jenyka_dm10 wrote:

Am I better off using bowtie2? Or bowtie is good enough, and i can keep using it?

Thanks!

ADD COMMENTlink written 5 months ago by jenyka_dm10
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