Ascaris suum raw RNA-Seq data
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Saheed Bachu
May 19, 2015, 1:04:15 PM5/19/15
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I noticed there is processed RNA-Seq data available for A. suum (http://nematode.net/NN3_frontpage.cgi?navbar_selection=funcexp&subnav_selection=microarray)
but after unzipping it, it looks like a binary file...? How do I "uncompress" it to view the contents?
Also, is the the raw data and annotation file available elsewhere? Thanks.
but after unzipping it, it looks like a binary file...? How do I "uncompress" it to view the contents?
Also, is the the raw data and annotation file available elsewhere? Thanks.
John Martin
Aug 5, 2015, 6:07:56 PM8/5/15
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Saheed,
My apologies for the long delay in replying to your question. The RNAseq data we have available via Nematode.net are a matrix of DCPM values per gene per sample/tissue, and a word document describing the expression experiment. Both of those files are compressed using UNIX 'gzip'. Once uncompressed, the processed data file should be plain text, and the methods file should be a word document. I'm wondering if maybe the tool you used for unzipping the file doesn't recognize unix 'gzip'? If you have access to unix/linux, the command to decompress is gunzip <file>. In Windows, standard decompression tools such as WinRAR or 7-Zip should be able to extract unix gzip files. And on a Mac, the Stuffit Expander should work.
Were you maybe looking at the word document? I think our website mislabels that file as a 'compressed textfile', but actually it extracts into a word document. If you were trying to open that file in notepad or something, that would look binary I think. You'd need to open that one in Word.
Regarding the Raw data, you can download all the A.suum RNAseq data that we've submitted from the NCBI SRA. I've attached a .csv file listing the 98 SRR ids that represent all the A.suum RNAseq we've produced. And I don't see an annotation file associated with A.suum RNAseq.
John Martin
My apologies for the long delay in replying to your question. The RNAseq data we have available via Nematode.net are a matrix of DCPM values per gene per sample/tissue, and a word document describing the expression experiment. Both of those files are compressed using UNIX 'gzip'. Once uncompressed, the processed data file should be plain text, and the methods file should be a word document. I'm wondering if maybe the tool you used for unzipping the file doesn't recognize unix 'gzip'? If you have access to unix/linux, the command to decompress is gunzip <file>. In Windows, standard decompression tools such as WinRAR or 7-Zip should be able to extract unix gzip files. And on a Mac, the Stuffit Expander should work.
Were you maybe looking at the word document? I think our website mislabels that file as a 'compressed textfile', but actually it extracts into a word document. If you were trying to open that file in notepad or something, that would look binary I think. You'd need to open that one in Word.
Regarding the Raw data, you can download all the A.suum RNAseq data that we've submitted from the NCBI SRA. I've attached a .csv file listing the 98 SRR ids that represent all the A.suum RNAseq we've produced. And I don't see an annotation file associated with A.suum RNAseq.
John Martin
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