Question: Which file can be upload in MG-RAST
0
gravatar for hafroz01
18 months ago by
hafroz010
hafroz010 wrote:

Hi,

I would like to use MG-RAST to analyse metagenomic data from paddy soils. I have got the forward (R1) and reverse (R2) fastq files and the file size is aound 20GB (for each R1 and R2). I read some papers and they used denovo assembler first to make the contigs and then uploaded the contigs file. Should I upload the join.fastq files (40GB each) without any denovo assembly (as MG-RAST has Join paired-ends option)? Could anyone please let me know?

Thanks Hasina

mg-rast metagenome assembly • 1.4k views
ADD COMMENTlink modified 18 months ago • written 18 months ago by hafroz010

Hi Sej Modha, Thanks for your response. I already uploaded the joined fastq files 4 days ago, still the files are in the queue for the first step (qc-stats) out of 22 steps of MG-RAST analysis. That's why I was wondering how long it will take to finish the analysis?

N.B: The file size I uploaded is really very big (40GB).

Hasina

ADD REPLYlink modified 18 months ago • written 18 months ago by hafroz010

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under @Sej's answer.

ADD REPLYlink written 18 months ago by genomax70k
0
gravatar for Sej Modha
18 months ago by
Sej Modha4.3k
Glasgow, UK
Sej Modha4.3k wrote:

Taken from the MG-RAST manual: ftp://ftp.metagenomics.anl.gov/data/manual/mg-rast-manual.pdf

MG-RAST users can upload raw sequence data in fastq, fasta and sff format; the sequences will be normalized (quality controlled) and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes, individually or in groups. Access to the data is password protected unless the owner has made it public, and all data generated by the automated pipeline is available for download in variety of common formats.

ADD COMMENTlink written 18 months ago by Sej Modha4.3k

I am not sure about the processing time for the MG-RAST but it is not clear whether you have got any assembled contigs or resources to assemble the contigs from fastq files. If you do have assembled contigs then you should upload the contigs to the MG-RAST server for further analysis.

ADD REPLYlink written 18 months ago by Sej Modha4.3k

Hi, I have already got the assembled contigs using Abyss. Here is the stats of the contigs ...... N50 229 Max_contig_size 56823, Number of bases in contigs 70700671, Number of contigs 275108, Number of contigs >=1kb 1590 Number of contigs in N50 99746, Number of bases in contigs >=1kb 3446405, GC Content of contigs 64.8125447069661

Here, the no of contigs 275108. Should I upload this contig file directly in MG-RAST? Because, I have found some other people reported the problems with high contigs no while uploading in MG-RAST. But, did not get the proper answer, how many contigs can be uploaded in MG-RAST? Could you please explain it?

ADD REPLYlink written 18 months ago by hafroz010
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