[mira_talk] Re: SFF_EXTRACT
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 2 Jun 2014 11:28:47 +0100
That version of sff_extract uses the -o option as the actual
filename, rather than as a prefix. Try:
./sff_extract sample1.sff -o sample.fastq
Or just rename your 'sample' file to 'sample.fastq'.
Peter
On Mon, Jun 2, 2014 at 10:59 AM, Bobby Paul <bobbypaul29@xxxxxxxxx> wrote:
> Dear Peter,
>
> Thank you very for your quick reply.
>
> I used sff_extract from seq_crumbs and version: 0.1.8.
>
> There is no error message but it generated one file named sample (without
> any file extension). Its looks like fastq file.
>
>
> Thanks
> Bobby Paul
>
>
> On Mon, Jun 2, 2014 at 3:20 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
> wrote:
>>
>> Hello Bobby,
>>
>> Which version of sff_extract do you have? Where did you get it from?
>> (This matters, the default settings have changed).
>>
>> Is there any output on screen? e.g. an error message?
>>
>> Are you sure no output files are being generated?
>>
>> Peter
>>
>>
>> On Mon, Jun 2, 2014 at 10:40 AM, Bobby Paul <bobbypaul29@xxxxxxxxx> wrote:
>> > Dear Sir,
>> >
>> > I am working on ion torrent data. I used sff_extract to get the sequence
>> > fasta. But it not generating any sequence file, fastq file or traceinfo
>> > file.
>> >
>> > Code used:
>> > ./sff_extract sample1.sff -o sample
>> >
>> > Please help me.
>> >
>> >
>> > Thanks,
>> >
>> > Bobby
>>
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>
>
>
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