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yhwu / idemp

Barcode demultiplex for Illumina I1, R1, R2 fastq.gz files
GNU General Public License v2.0
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trouble demultiplexing #3

Open reidgrahamgriggs opened 7 years ago

reidgrahamgriggs commented 7 years ago

I'm trying to demultiplex illumina paired end 2*250 data. I have a single forward fastq file and a single reverse fastq file and a mapping file, but no index reads file. I tried creating an index reads file with QIIME using the extract barcodes file, but dont think its in the right format because I could only take it from the forwards reads. We used the emp formate described here (http://www.earthmicrobiome.org/emp-standard-protocols/16s/) whereby there is only a barcode on the forward sequences. My thought is that you should be able to demultiplex the reverse reads by associating the lane id/index id with the sample id after demultiplexing the forward reads accordign to the barcode file & sample ids. Can your software do this/do you have any suggestions as to how I might proceed?

As your software is running in the current state, I'm getting an output like this where the sample ids are not matched TYGNS0104:TYGNS0101 TYGNS0104:TYGNS0102 TYGNS0104:TYGNS0103 TYGNS0105:TYGNB0105 TYGNS0105:TYGNS0101 TYGNS0105:TYGNS0102 TYGNS0105:TYGNS0103 TYGNS0105:TYGNS0104

Thanks for any and all help.

yhwu commented 7 years ago

Please take a look at the example fastq files for R1, R2, and I1 files. The reads and the indices must match. I am not sure what QIIME give you, so it's hard to say what went wrong. ...Yinghua

On Fri, Feb 3, 2017 at 12:56 AM, reidgrahamgriggs notifications@github.com wrote:

I'm trying to demultiplex illumina paired end 2*250 data. I have a single forward fastq file and a single reverse fastq file and a mapping file, but no index reads file. I tried creating an index reads file with QIIME using the extract barcodes file, but dont think its in the right format because I could only take it from the forwards reads. We used the emp formate described here (http://www.earthmicrobiome.org/emp-standard-protocols/16s/) whereby there is only a barcode on the forward sequences. My thought is that you should be able to demultiplex the reverse reads by associating the lane id/index id with the sample id after demultiplexing the forward reads accordign to the barcode file & sample ids. Can your software do this/do you have any suggestions as to how I might proceed?

As your software is running in the current state, I'm getting an output like this where the sample ids are not matched TYGNS0104:TYGNS0101 TYGNS0104:TYGNS0102 TYGNS0104:TYGNS0103 TYGNS0105:TYGNB0105 TYGNS0105:TYGNS0101 TYGNS0105:TYGNS0102 TYGNS0105:TYGNS0103 TYGNS0105:TYGNS0104

Thanks for any and all help.

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