Question: FastqToSam (Picard) syntax paired-end reads
gravatar for esteban.peguero
6 weeks ago by
esteban.peguero0 wrote:

Do you know what is the FastqToSam (Picard) syntax when using paired-end and the option "--USE_SEQUENTIAL_FASTQS"?

In the help section they provide an example:

"Use sequential fastq files with the suffix _###.fastq or _###.fastq.gz.The files should be named: _001., _002., ..., _XYZ. The base files should be: _001. An example would be: RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R1_003.fastq RUNNAME_S8_L005_R1_004.fastq RUNNAME_S8_L005_R1_001.fastq should be provided as FASTQ."

I assume that in the case of paired-end it would be something like:

RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R2_001.fastq 
RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R2_002.fastq

would that be correct?

sequencing rna-seq • 127 views
ADD COMMENTlink modified 6 weeks ago by h.mon31k • written 6 weeks ago by esteban.peguero0

Yes, but this splitting of files is uncommon nowadays. This was common when files were often transferred by ftp, ad internet speed was slower.

ADD REPLYlink written 6 weeks ago by h.mon31k

Thanks for the reply. In this case, I need to use this syntax because I'm using picard on a third-party platform that only supports one FASTQ input port.

ADD REPLYlink written 6 weeks ago by esteban.peguero0

You could cat the pieces together to make two inputs. R1_001, R1_002 etc go to R1.fastq. Make sure you use the same order in both R1/R2 files.

ADD REPLYlink written 6 weeks ago by genomax89k
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