Input filename

[dridk]

Hi,

Could you describe the format of input fastq ?
Is there an exemple somewhere ?

[plaffy]

Hi Sacha
Fastq format is a standard sequencing file format which is the general output of illumina sequencing data
details on its structure can be found here
https://en.wikipedia.org/wiki/FASTQ_format
does this answer your question?
Patrick

[dridk]

Hi Thanks for your reply. I Know about fastq. I m asking you what are arguments of your scripts. It seems it looks into a folder and process all fastq inside . But How to name these file? A brief exemple of how you run your files will be greate. Thanks Le 4 déc. 2016 23:35, "plaffy" <notifications@github.com> a écrit :

…

Hi Sacha Fastq format is a standard sequencing file format which is the general output of illumina sequencing data details on its structure can be found here https://en.wikipedia.org/wiki/FASTQ_format does this answer your question? Patrick — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB0pF1bn86lNuM4IQZeFltOPyxi3Mhyuks5rE0BBgaJpZM4LCpA_> .

[plaffy]

so you name your input folder within the configfile.txt
the fastq files should be paired end data, with reads separated into the two separate files
the only naming convention we use to discern which file is which in our analysis is the filenames must have either "R1" or "R2" somewhere within their filename.
the rest of the name should be identical
an example would be the following files:
sample1.96650_S1_L001_R1_001.fastq.gz
sample1.96650_S1_L001_R2_001.fastq.gz

does this help?

[dridk]

Yes thanks you. That what I need. Will test it! Thanks . Le 4 déc. 2016 23:57, "plaffy" <notifications@github.com> a écrit :

…

so you name your input folder within the configfile.txt the fastq files should be paired end data, with reads separated into the two separate files the only naming convention we use to discern which file is which in our analysis is the filenames must have either "R1" or "R2" somewhere within their filename. the rest of the name should be identical an example would be the following files: sample1.96650_S1_L001_R1_001.fastq.gz sample1.96650_S1_L001_R2_001.fastq.gz does this help? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB0pFy6yTHUgAPtGFyEPBFbYvAPjSqZxks5rE0VxgaJpZM4LCpA_> .