Ion Torrent PGM data analysis (BMP)
Hello,
I recently started using the Brazilian Microbiome Project pipeline (http://www.brmicrobiome.org/#!16sprofilingpipeline/cuhd) for 16s rRNA gene profiling with my Ion Torrent data and I came across some problems, which I think are related with the data, and not the scripts in particular, but I was hoping that someone could give me some suggestions, given the fact that I am still new in the field of bioinformatics and only used the standard QIIME workflow with 454 data.
I have 10 fastq files corresponding to 10 different samples and they have already been pre-processed before getting to me, and both barcodes and forward primers were trimmed. However, I don't think any quality filtering step has been performed, so what I did was to perform quality filtering in each of the fastq files, converted them into fasta files, added sampleID labels, and merged all the fasta files into one only fasta file. Then I proceeded as the pipeline suggested, but my I don't think my "results.biom.table" file looks as it is supposed to look and I don't know what other alternatives I have. I attach a .txt file with what I did, as well as a snapshot of the "results.biom.file", since apparently I cannot upload it.
I would like to have the raw .sff or .fastq file that comes out of the sequencer, so that I could perform something like split_libraries_fastq.py (QIIME) or fastq_strip_barcode_relabel2.py (UPARSE), but then my samples would only be 10 among all the remaining ones that were run simultaneoulsy in the chip and I don't have any information regarding them.
I hope I managed to make myself clear. As I mentioned, I am still new at this, and maybe there's a very simple way to solve this.
Another thing: Has anyone used the new script multiple_split_libraries_fastq.py that comes with the candidate version of QIIME 1.9.0 with PGM 16s data?
Thank you very much in advance,
Joana
I recently started using the Brazilian Microbiome Project pipeline (http://www.brmicrobiome.org/#!16sprofilingpipeline/cuhd) for 16s rRNA gene profiling with my Ion Torrent data and I came across some problems, which I think are related with the data, and not the scripts in particular, but I was hoping that someone could give me some suggestions, given the fact that I am still new in the field of bioinformatics and only used the standard QIIME workflow with 454 data.
I have 10 fastq files corresponding to 10 different samples and they have already been pre-processed before getting to me, and both barcodes and forward primers were trimmed. However, I don't think any quality filtering step has been performed, so what I did was to perform quality filtering in each of the fastq files, converted them into fasta files, added sampleID labels, and merged all the fasta files into one only fasta file. Then I proceeded as the pipeline suggested, but my I don't think my "results.biom.table" file looks as it is supposed to look and I don't know what other alternatives I have. I attach a .txt file with what I did, as well as a snapshot of the "results.biom.file", since apparently I cannot upload it.
I would like to have the raw .sff or .fastq file that comes out of the sequencer, so that I could perform something like split_libraries_fastq.py (QIIME) or fastq_strip_barcode_relabel2.py (UPARSE), but then my samples would only be 10 among all the remaining ones that were run simultaneoulsy in the chip and I don't have any information regarding them.
I hope I managed to make myself clear. As I mentioned, I am still new at this, and maybe there's a very simple way to solve this.
Another thing: Has anyone used the new script multiple_split_libraries_fastq.py that comes with the candidate version of QIIME 1.9.0 with PGM 16s data?
Thank you very much in advance,
Joana