SDM demultiplexing issue for paired end fastq file

[sonumu...@gmail.com]

Dear Falk,

I am trying to achieve demultiplexing for for illumina seqeunce data using SDM. I have paired end fastq files (R1 and R2; both in mix orientation of reads) and need to generated demultiplexed per sample based R1 and R2 fastq files. MIDs are attached in both end of the reads. I am running following command but it seems only one R1 fastq file is been read by the program and only one pair is generated in the output?

Let me know how we can use SDM in this situation.

Regards

Sunil

sdm -i_fastq PKBacP1_S1_L001_R1_001.fastq -map Mapfil_PKBacP1.txt -paired2 PKBacP1_S1_L001_R2_001.fastq -saveDemultiplex 1 -o_demultiplex Demult_PKBac1/ 

[Falk Hildebrand]

Hey Sunil,

there is no second fastq file given, the sdm syntax is actually different. E.g. "-paired2" is not a supported flag. 

What you probably want is:

sdm -i_fastq PKBacP1_S1_L001_R1_001.fastq,PKBacP1_S1_L001_R2_001.fastq -map Mapfil_PKBacP1.txt  -saveDemultiplex 1 -o_demultiplex Demult_PKBac1/ 

let me know if this worked,

Falk