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Question: Less reads when uploading to galaxy
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gravatar for mvinas
17 months ago by
mvinas • 20
mvinas • 20 wrote:

Hello,

I am trying to upload files which contains, each, about 40 millions of reads (~2GB each, file format: fastq.bz2). But when I upload them from the ftp server, not all reads, and only some of them (only 4200 sequences) appears in the file in Galaxy.

What can be the reason?

Thank you in advance,

Maria Vinas
rna-seq • 460 views
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modified 16 months ago • written 17 months ago by mvinas • 20
1
gravatar for mvinas
16 months ago by
mvinas • 20
mvinas • 20 wrote:

Thanks Jen,

I found the problem. Galaxy was recognizing the wrong format. I set the correct type of format (fastq.bz2) before loading the data and it worked!.

Maria Vinas
ADD COMMENT • link written 16 months ago by mvinas • 20
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gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Double check that the FTP load was complete. You might also try uncompressing the file locally to double check that it contains all of the expected data. If all else fails, loading the data uncompressed is also an option.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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