Unequal size output fastq files

[cheng0712]

Hi,

I have some paired end data, and I get the demultiplexed fastq files by the following command: _idemp -b map.txt -I1 lane1_NoIndex_L001_R2_001.fastq.gz -R1 lane1_NoIndex_L001_R1_001.fastq.gz -R2 lane1_NoIndex_L001_R3001.fastq.gz -m 2 -o lane1/

But I am surprised to see some samples have outputs of unequal size fastq files. Are you matching the barcodes with the forward reads and reverse reads separately or simultaneously?

Thanks, Cheng

[yhwu]

Mapping is done only once on the index read, each read in R1 and R2 are assigned to a file according to the mapping. So, I don't know why you got error. Could be a bug. I'd try

idemp -b map.txt -I1 lane1_NoIndex_L001_R2_001.fastq.gz -R1 lane1_NoIndex_L001_R1_001.fastq.gz -m 2 -o lane1/
idemp -b map.txt -I1 lane1_NoIndex_L001_R2_001.fastq.gz -R2 lane1_NoIndex_L001_R3_001.fastq.gz -m 2 -o lane1/

to see whether you could get correct results. It seems you have Hiseq. I haven't tested it on that platform. So, results could be totally wrong.

[cheng0712]

It is ATAC-seq data. There is no difference between your codes and mine. BTW, what is your definition of mismatch? Partially matched?

[yhwu]

It's hard to know what went wrong without a piece of you data to reproduce the error. Mismatch includes base pair mismatch, deletion, insertion.

[J-Sabino]

Hi, I have Hiseq data and I am having the same problem. Have you already tested idemp with Hiseq data? Are you planning to test it?

[yhwu]

MiSeq only. It won't work on Hiseq.