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Short Read Sequence Typing for Bacterial Pathogens
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Analyzing NextSEq data #35

Closed tomitaMDU closed 9 years ago

tomitaMDU commented 9 years ago

Hi Kat,

I got NextSeq data which contains 4X forward fastq files and 4X reverse fastq files, in total 8 files for each sample. I concatenated 4 forward fastq files and 4 reverse fastq files to one forward and reverse fastq files, and run SRST2 but it seems like not processing the run.

Please tell me how to handle such multiple fastq files for SRST2.

Best regards, Tomi

ppcherng commented 9 years ago

Hi Tomi,

I've never run SRST2 with any NextSeq data, but I have run with a bunch of paired end fastq files concatenated to each other seemingly without problems. What are the commands you're running and what error message are you getting?

-Paul

tomitaMDU commented 9 years ago

Hi Paul,

I tried last week and used brantfairclothhttps://gist.github.com/brantfaircloth / merge_next_seq.pyhttps://gist.github.com/brantfaircloth/d69387a8fe3e8eae9860 https://gist.github.com/brantfaircloth/d69387a8fe3e8eae9860, then SRST2 worked nicely.

Thank you very much. Best regards,

Takehiro Tomita, PhD

Molecular Scientist

Microbiological Diagnostic Unit - Public Health Laboratory Department of Microbiology & Immunology Peter Doherty Institute for Infection and Immunity The University Of Melbourne

Address: Level 1,792 Elizabeth Street (Corner of Grattan & Elizabeth Streets) Melbourne 3010 Department of Microbiology & Immunology The University of Melbourne at Peter Doherty Institute for Infection and Immunity – Enter Foyer and take a lift to Level 1.

Phone 1:+61 3 83445713 Phone 2:+61 3 83445701 Fax: +61 3 83447833

From: ppcherng [mailto:notifications@github.com] Sent: Wednesday, 18 March 2015 6:01 PM To: katholt/srst2 Cc: Takehiro Tomita Subject: Re: [srst2] Analyzing NextSEq data (#35)

Hi Tomi,

I've never run SRST2 with any NextSeq data, but I have run with a bunch of paired end fastq files concatenated to each other seemingly without problems. What are the commands you're running and what error message are you getting?

-Paul

— Reply to this email directly or view it on GitHubhttps://github.com/katholt/srst2/issues/35#issuecomment-82786054.