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jiwoongbio / FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
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Comparison usage #6

Open VictorBorin opened 6 years ago

VictorBorin commented 6 years ago

Hello, Thank you for the excellent pipeline tool.

I have a question about the FMAP_comparison.pl. I have 4 samples in duplicate, how i can run the comparison step (sample group information) ?

Thanks.

jiwoongbio commented 6 years ago

I am sorry for the late reply. You can put the sample groups as separate arguments like following:

perl FMAP_comparison.pl abundance_table.txt control1,control2,control3,control4 case1,case2,case3,case4 > comparison.txt

Before this command, you need to generate a table file using "FMAP_table.pl".

Thanks.

VictorBorin commented 6 years ago

Hello again, and thank you for the answer. I have another question. I try to put my reads files in the command perl FMAP_assembly.pl, but he returns the follow error: ERROR in FMAP_assembly.pl: wb_R1_all.fq.gz,/wb_R2_all.fq.gz' is not readable. The reads are from 8 samples merged, beacause i did co-assembly in megahit. When I do the samples separated, it's work normal.

Thanks

jiwoongbio commented 6 years ago

Hello, Can you share the full command you used? I think you could put a wrong FASTQ file path and it should be like "wb_R1_all.fq.gz,wb_R2_all.fq.gz". Thank you.

VictorBorin commented 6 years ago

Hello, I managed to find my mistake: I tried to run FMAP with the out at the end: perl FMAP_assembly.pl final.contigs.fa wb_R1_all.fq.gz,wb_R2_all.fq.gz ../wb_megahit

And the right is: perl FMAP_assembly.pl ../wb_megahit final.contigs.fa wb_R1_all.fq.gz,wb_R2_all.fq.gz

Thank you

jiwoongbio commented 6 years ago

Thank you :)