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Forum: Bioinformatics 10-03-2013, 12:20 PM
Replies: 2
Views: 7,439
Posted By szimmerman
Thank you and follow up question about coverage plot

Thanks a lot for the response. I got it to work doing what you said. However, I figured that the dot plot is not actually what I want, since I am comparing many query contig sequences that map to a...
Forum: Bioinformatics 09-19-2013, 09:04 PM
Replies: 2
Views: 7,439
Posted By szimmerman
mummerplot unable to generate graphic

Hi everyone,

So I used nucmer and successfully generated a .delta file. Then, I tried to run mummerplot using the command

mummerplot ref_qry.delta -R ham_pb4_shred_2k.utg.fasta -Q...
Forum: Bioinformatics 08-01-2013, 07:03 AM
Replies: 2
Views: 1,546
Posted By szimmerman
Thanks a lot!

Thanks a lot!
Forum: Bioinformatics 07-31-2013, 04:47 PM
Replies: 2
Views: 1,546
Posted By szimmerman
mira assembly error

Hi everyone,

So I was doing a hybrid assembly with mira using a pacbio assembly as the backbone and Illumina reads in a .fasta file. Along with that fasta file, I have a .qual file, but it does...
Forum: Bioinformatics 07-25-2013, 07:49 PM
Replies: 2
Views: 5,330
Posted By szimmerman
Reptile comes with a program to turn fastq reads...

Reptile comes with a program to turn fastq reads into a format it can read. Look at this tutorial for details.

http://aluru-sun.ece.iastate.edu/doku.php?id=reptile_tutorial
Forum: Bioinformatics 07-23-2013, 08:42 AM
Replies: 4
Views: 1,853
Posted By szimmerman
SSPACE help

Hi everyone,

I was just wondering what an f_tig meant in the .evidence file produced by SSPACE. Is it the original contigs that are put into a scaffold or something else? Thanks!
Forum: Bioinformatics 07-23-2013, 07:14 AM
Replies: 1
Views: 2,162
Posted By szimmerman
SOAPdenovo issue

Hi everyone,

I am getting some strange results after using SOAPdenovo. First I run prepare, then I run map and scaff like usual. My problem is, that I load 6886 contigs into the scaff, but then...
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