Re: [galaxy-user] How should I include biological replicates in cufflink/cuffdiff?
> My question is, if I need to compare between 5 time points, should I do > comparison pairwise? No, do them all at once with Cuffdiff: (a) set 'Perform Replicate Analysis' to 'Yes'; (b) create 5 replicate conditions, one for each time point; (c) add your replicates for each time point. There's a Cuffdiff flag to do time series analysis, but it isn't implemented yet in Galaxy, so you'll get pairwise comparisons for all conditions. You can use the filtering tool to reduce Cuffdiff outputs to only the timepoint comparisons. > I will use cuffmerge to merge 0hour-1, 0hour-2, 0hour-3, > 1hour-1,1hour-2.1hour-3 to generate one cuffmerge file. Correct. > Then I will run cuffdiff using the merged file, include two groups, group 1 > is 0 hour (add 0hour 1-3 in group 1) and group 2 is 1hour (add 1hour1-3 in > group 2). Use the process I described above to do all pairwise comparisons in one run. Good luck, J. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Using BWA to map without any mismathces
Hello, We have a sample containing several bacterial species and we want to uniquely map RNA-seq reads to the genomes of each of our organisms to get the expression patterns of each organism separately. We tried to use BWA in Galaxy with the “edit distance” (aln -n in the command line version) set to 0 but none of the reads were mapped (all had the SAM tag set to “4’). This is an artifact since running BLAST with some of the sequences showed that they have 100% identity to one of our genomes and not any others, so they should map uniquely. When running BWA with the number of mismatches set to between 1-5 >90% of our reads were mapped, and the number of mapped reads increased with the mismatch number so that seems to be working OK. Does the "aln -n" option really determine the number of mismatches? Any ideas why BWA will not run well in Galaxy using –n=0? Thanks Daniel -- ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
