BOL: Question: WHich method is best to convert pacBio reads in .sra format to .fastq format?

Question: Question: WHich method is best to convert pacBio reads in .sra format to .fastq format?

Nadia Baig
2006 days ago

Question: WHich method is best to convert pacBio reads in .sra format to .fastq format?

i am using fastq dump to convert sra files into fastq.

In case of fastq this tool gives me a message on terminal "Ignoring --- number of reads as the spot length is less than 1"). if my sra file is of 6GBs, i always get fastq file less than the afforementioned size. Ideally it must be a larger fastq file (~10gbs).Why is this so?

Answers

Can you please share your command used ?

Rahul Nayak 2006 days ago

fastq-dump --split-spot path/to/local/file/SRR649944.sra

Nadia Baig 2005 days ago

you have to use "-M 0" or else end up with unpaired reads, due to fastq-dump discarding small reads but keeping its pair.

— Rahul Nayak 2003 days ago

I always prefer EBI: This way is better than fastq-dump. EBI has fastq files to squarely download and use.

got to EBI http://www.ebi.ac.uk/ena/data/view/SRR121576

replace SRR121576 with your id name.

By the way , did you tried this

fastq-dump --split-3 *.sra

Neel 2003 days ago

I guess this is for paired end data. I have single end pacbio reads. Anyways thanks !

— Nadia Baig 2003 days ago

It works for bith type of data ...

--split-3 will output 1,2, or 3 files: 1 file means the data is not paired. 2 files means paired data with no low quality reads or reads shorter than 20bp. 3 files means paired data, but asymmetric quality or trimming.

— Neel 2003 days ago

Okay I will try thanks.

Nadia Baig 2002 days ago

BOL

Nadia Baig

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Question: Question: WHich method is best to convert pacBio reads in .sra format to .fastq format?