Hi Matt,
I want to concentrate on one selected bacterium to conduct phylogenetic analysis in different gut metagenome samples. So first, I ran inStrain profile ./sample.sam ./assembly.part_contig_1.fasta -o ./sample.IS -p 60 .However, in some samples the output sample.IS has files in output folder while some samples have no files in output folder. All the figure folders of all samples are completely empty.
I'm not entirely sure whether this situation is caused by the fasta file I provided. Since we are interested in this bacterium, we conducted third-generation sequencing, which means there is only one sequence with a length of 2MB in the input fasta.
After finishing the inStrain profile step, i want to use inStrain compare -i ./sample1.IS/ ./sample2.IS/ -p 6 -o ./combine_test.IS.COMPARE for further analysis.
However, the result only contains combine_test.IS.COMPARE_comparisonsTable.tsv in the output folder of combine_test.IS.COMPARE. I'm wondering if this workflow of mine is reasonable? What additional steps should I add? Which output file do you recommend for phylogenetic analysis?"
Hi Matt, I want to concentrate on one selected bacterium to conduct phylogenetic analysis in different gut metagenome samples. So first, I ran
inStrain profile ./sample.sam ./assembly.part_contig_1.fasta -o ./sample.IS -p 60.However, in some samples the output sample.IS has files in output folder while some samples have no files in output folder. All the figure folders of all samples are completely empty.I'm not entirely sure whether this situation is caused by the fasta file I provided. Since we are interested in this bacterium, we conducted third-generation sequencing, which means there is only one sequence with a length of 2MB in the input fasta.
After finishing the inStrain profile step, i want to use
inStrain compare -i ./sample1.IS/ ./sample2.IS/ -p 6 -o ./combine_test.IS.COMPAREfor further analysis.However, the result only contains
combine_test.IS.COMPARE_comparisonsTable.tsvin the output folder ofcombine_test.IS.COMPARE. I'm wondering if this workflow of mine is reasonable? What additional steps should I add? Which output file do you recommend for phylogenetic analysis?"thanks a lot!