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Old 11-19-2014, 05:33 PM   #1
transforu
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Location: Taiwan

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Default fastq-dump

Hello:
I got paired-end reads from http://www.ncbi.nlm.nih.gov/sra/?term=ERR032965
, and decompress it with fastq dump --split-files, --split-spot .
But only Single-end appear. Why ??
Please Help me !
thanks!
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Old 11-19-2014, 11:44 PM   #2
dpryan
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Try --split-3. Also, you're guaranteed that samples with ERR... accession numbers are available in fastq format from ENA. That's usually easier than dealing with SRA.
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Old 11-20-2014, 03:07 AM   #3
GenoMax
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ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR032/ERR032965/
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Old 11-20-2014, 08:32 PM   #4
transforu
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Hi dpryan and GenoMax

Thanks for your help ! and i am return result

I have tried various argument for fastq-dump, it does not work too.

GenoMax teach me download it from ebi ftp,
But it is single-end reads too. and spots less then that files from NCBI !?

Thank you very much!
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Old 11-20-2014, 11:35 PM   #5
dpryan
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They only uploaded single-end data (101 base reads). My guess is that they just clicked the wrong box when they submitted the data. The files that GenoMax linked to are the originals, so what's there is what they actually submitted (rather than what they say they submitted).

BTW, you'll need to trim that dataset as a lot of the reads are really crappy.
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Old 12-11-2014, 09:22 AM   #6
osris
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Quote:
Originally Posted by transforu View Post
Hello:
I got paired-end reads from http://www.ncbi.nlm.nih.gov/sra/?term=ERR032965
, and decompress it with fastq dump --split-files, --split-spot .
But only Single-end appear. Why ??
Please Help me !
thanks!
sra-stat --xml --statistics ERR032965 shows this run is not paired.
<Statistics nreads="2" nspots="34127049">
<Read index="0" count="34127049" average="101" stdev="0" />
<Read index="1" count="0" average="0" stdev="0" />
</Statistics>
second read (index=1) is empty. the metadata is incorrect.
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