Allpaths-LG help

[duf]

Hello. Where can I find some simple test data other than test.genome for ALLPATHS-LG? Their test genome worked fine but I have an assignment to assemble something else. Part of the assignment is to find data myself.
I went to their ftp://ftp.broadinstitute.org/pub/ but I'm kind of lost there.
I need something small and simple to assemble if possible, as I'm a newbie student.
Thank you so much.
Duf

[ucpete]

The Short Read Archive has *tons* of free sequence data available:

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=download_reads

If you can assembly anything, go for a microbial or viral genome.

[duf]

Thanks for your quick reply. These are sra files and I need to convert them, right? How do I know which organism it is? They seem to have names like
DRR000558

For example here:
ftp://ftp-trace.ncbi.nlm.nih.gov/sra...279/DRR000558/
Or am I completely wrong?

[ucpete]

Use the search tab if you're looking for something in particular. If you want to assemble the Illumina control sequence data, search for phi X and you'll find data like this:

http://www.ncbi.nlm.nih.gov/sra/SRX025876

I realize that Allpaths-LG is for large genomes, so maybe you want to go after a eukaryotic genome instead? You can browse by experiment type, etc. I urge you to poke around a bit.

[duf]

Thanks! that's a good starting point for me.
I'll try tomorrow one of them at school.

[ucpete]

To answer your other question, you'll download the .sra or .sralite file for the run, and you'll likely need to install and run fastq-dump to convert the data to FASTQ. More information on that can be found here:

http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.5_Converting_SRA_for

[krueml]

Hello,

I didn't want to open a new thread, but I need help in my situation. I have whole genome data of a human sequenced by illumina and I have a problem with the library settings in_lib.csv. I downloaded GRCh37 from http://hgdownload.cse.ucsc.edu/golde...chromFa.tar.gz. Now I have all the .fa-files from each chromosom. How do I put them into the library? Or do I have to merge them first? So how do the lines in in_lib.csv look like then?

Thank you