I have a MiSeq fastz.gz file, what to do with it

[KnowNothing2]

I hear I need to assess it using bowtie, but when I download that program on Windows I can't even get it to open. How to I evaluate my reads?

[aaronh]

Sounds like the first thing you need to do is work through something like http://ged.msu.edu/angus/ or http://intro-prog-bioinfo-2013.wikispaces.com/ Step 0 is to use Ubuntu or some kind of linux.

[dpryan]

Alternatively, familiarize yourself with Galaxy.

[GenoMax]

Start by looking at the tutorials at Galaxy here: http://wiki.galaxyproject.org/Learn/Screencasts. As Devon suggested it is a biologist friendly way of using command line tools in a browser.

You can do independent QC assessment of your sequence data by using a tool such as FastQC: http://www.bioinformatics.babraham.a...ojects/fastqc/ This will run on windows.

At some point you will want to get a broader understanding of NGS: http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29

[KnowNothing2]

Alternatively, familiarize yourself with Galaxy.

Is this a work around to have a Unix-based system? (i.e. can I use galaxy without installing a Unix system?)

[winsettz]

Is this a work around to have a Unix-based system? (i.e. can I use galaxy without installing a Unix system?)

Yep, that's what Galaxy was intended for.

An option is to try a Linux VM, but you'll be limited by the performance of your workstation. Generally in an academic institution there are computing resources available depending on your line of work...

[KnowNothing2]

Is there a way to transfer from BaseSpace to Galaxy? It seems uploading from my computer is taking forever

[GenoMax]

If you already have data in basespace why not do the analysis there? After all that is the purpose of basespace.

To answer your question .. if you are able to generate a unique URL (with either no password or embedded password) for your base space file you may be able to transfer it directly to galaxy using this method: http://wiki.galaxyproject.org/Support#Loading_data

[KnowNothing2]

If you already have data in basespace why not do the analysis there? After all that is the purpose of basespace.

To answer your question .. if you are able to generate a unique URL (with either no password or embedded password) for your base space file you may be able to transfer it directly to galaxy using this method: http://wiki.galaxyproject.org/Support#Loading_data

Oh, I didn't know I could do analysis in BaseSpace. I thought it was just a cloud based system that my Uni used to store data.

Looks like BaseSpaces programs cost extra money...

[GenoMax]

Oh, I didn't know I could do analysis in BaseSpace. I thought it was just a cloud based system that my Uni used to store data.

Looks like BaseSpaces programs cost extra money...

Presumably BaseSpace could be used only as a storage system but it is possible to do analysis/share data in BaseSpace. See the BaseSpace manual: http://supportres.illumina.com/docum..._15044182a.pdf

Not having used BaseSpace I am not sure what analysis you can do at no cost. I assume there is some basic analysis (akin to what you can do on MiSeq itself e.g. alignments) available for free.

Note: If there are no "free" analysis tools in BaseSpace then I take my original suggestion of using BaseSpace back.

[winsettz]

Picard will only let you work on 100MB or less bam files for free. Anything above that is "1 iCredit".

Don't see a bowtie on basespace, but I do see a number of visualizers.

I suppose an option may be to compile bowtie2 on a linux VM, build the reference if one isn't available online, then map the reads yourself, but it depends on the computing resources you have on hand.

[KnowNothing2]

Presumably BaseSpace could be used only as a storage system but it is possible to do analysis/share data in BaseSpace. See the BaseSpace manual: http://supportres.illumina.com/docum..._15044182a.pdf

Not having used BaseSpace I am not sure what analysis you can do at no cost. I assume there is some basic analysis (akin to what you can do on MiSeq itself e.g. alignments) available for free.

Note: If there are no "free" analysis tools in BaseSpace then I take my original suggestion of using BaseSpace back.

IGV aligner (Broad Inst) is free through BaseSpace, but it only accepts BAM and VCF files and I have a FastQ. Is there an easy way to convert?

[KnowNothing2]

Picard will only let you work on 100MB or less bam files for free. Anything above that is "1 iCredit".

Don't see a bowtie on basespace, but I do see a number of visualizers.

I suppose an option may be to compile bowtie2 on a linux VM, build the reference if one isn't available online, then map the reads yourself, but it depends on the computing resources you have on hand.

Bowtie is through Galaxy, which I'm also in the process of trying to get my data uploaded on to.

[dpryan]

IGV aligner (Broad Inst) is free through BaseSpace, but it only accepts BAM and VCF files and I have a FastQ. Is there an easy way to convert?

Not in the way that you want. You'd need to align the reads, which is presumably possible on basespace, but perhaps isn't free.

[KnowNothing2]

Picard will only let you work on 100MB or less bam files for free. Anything above that is "1 iCredit".

Don't see a bowtie on basespace, but I do see a number of visualizers.

I suppose an option may be to compile bowtie2 on a linux VM, build the reference if one isn't available online, then map the reads yourself, but it depends on the computing resources you have on hand.

Bowtie is through Galaxy, which I'm also in the process of trying to get my data uploaded on to.