How to use Galaxy to obtain read counts from SRA files
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7.4 years ago
statfa ▴ 750

Hi,

Does anyone know how I can obtain read counts from SRA files using Galaxy? For some reasons, I can't download the SRA files on my computer and I have to obtain read counts using some online solutions...

Thanks in advance

This question is related to my previous question here: (A: obtain RNA-seq read counts online)

Galaxy read count SRA file • 3.5k views
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While I understand that limitations of local hardware prevent you from downloading the original data and processing it yourself, by using an online solution you are limiting yourself to programs available on online resources (and the options they expose in the GUI). If you are comfortable with that limit then @harold had linked a tutorial for galaxy in the other thread you have open on this topic.

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Why can't you download the SRAs? Is it a problem with the download command, are the files too large for your computer, or is it something else?

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they are large to download and process on my computer

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Another option to avoid SRA, would be to download the raw sequences (fasta/fastq) from ENA: http://www.ebi.ac.uk/ena, if available. Then realign them using a splice aware aligner (STAR, tophat, HISAT...) and count the reads.

And as pointed by harold, try to better describe your problem.

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The problem is those files are too large to be processed on my computer... Downloading those files is not the optimum way... I heard from a friend that I don't need to download the files... there are some online methods to obtain read count from SRA files... When I asked my question on biostars, one suggested I can use Galaxy (https://www.biostars.org/p/212785/#212844)... That's why I'm looking for some tutorial

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I heard from a friend that I don't need to download the files

Perhaps you should ask this friend for his/her recommendations. If your intention is to perform your own analysis, you will have to download the files from SRA (perhaps not to your local computer, but definitely to the server running the analysis software).

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I guess he said he uses cloud... I don't know it well... I heard the name of two softwares from him: Galaxy and Bowtie... I don't access him but I remember he said you don't need to download the files... you can put the links of the files on that software and do the further analysis

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