Question: Cross assembly of metagenomics
0
gravatar for MAPK
15 months ago by
MAPK1.5k
Washington University in St. Louis
MAPK1.5k wrote:

I am working on metatranscriptomic data and wanted to use this tool available here: https://edwards.sdsu.edu/crass/# I have assembled my transcriptomic data using Trinity and have got Trinity.fasta file. However, this tool also requires ace format file, which I don't have. What do I need to do to get ACE file or specifically how do I run this program? I would really appreciate if someone clarifies.

rna-seq • 290 views
ADD COMMENTlink modified 3 months ago by onestop_data260 • written 15 months ago by MAPK1.5k

This tool is meant for situations where you have multiple assemblies, e.g. 10 gut microbiota assemblies from different people..

ADD REPLYlink written 15 months ago by 5heikki8.7k
0
gravatar for onestop_data
3 months ago by
onestop_data260
onestop_data260 wrote:

CrAss was designed for comparative metagenomics. You assemble all your metagenomes together, and the tool leverages the overlapping across samples to infer the distance within samples.

The tool first required an ACE file, but this not common anymore (I think MIRA assembler generated it as one of its outputs). Luckily it accepts SAM file (*) (not BAM) to replace the ACE file.

Here is a tutorial on how to run the tool step-by-step

(*) the SAM file reflects the maps all samples reads against the cross-assembly (contigs)

ADD COMMENTlink written 3 months ago by onestop_data260
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