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Forum: Bioinformatics 02-28-2017, 06:15 AM
Replies: 104
Views: 41,776
Posted By JVGen
Hi Brian, I'm running into a problem where...

Hi Brian,

I'm running into a problem where Tadpole is creating two contigs, yet the generated contigs have identical overlapping ends. I've shared the FASTA files and reads via Google Drive. The...
Forum: Bioinformatics 02-03-2017, 09:03 AM
Replies: 104
Views: 41,776
Posted By JVGen
Hi Brian, I was wondering if there was a way...

Hi Brian,

I was wondering if there was a way to save the reads that are used during contig assembly, so that they can be mapped back to the generated consensus in a downstream step. I noticed the...
Forum: Bioinformatics 01-17-2017, 03:46 PM
Replies: 104
Views: 41,776
Posted By JVGen
Thank you for the input, Brian. I tried bm1=8...

Thank you for the input, Brian. I tried bm1=8 bm2=2 earlier, as per info available on JGI's website. It unfortunately still splits, though I haven't tried bm1=6 yet. Of course, this is an instance...
Forum: Bioinformatics 01-17-2017, 01:58 PM
Replies: 104
Views: 41,776
Posted By JVGen
Hi Brian, Reads are 150x2, and I generally...

Hi Brian,

Reads are 150x2, and I generally have >100x coverage. I tried increasing to k=60, but that splits the input into many more contigs.

My goal here is to extract a consensus sequence...
Forum: Bioinformatics 01-17-2017, 12:52 PM
Replies: 104
Views: 41,776
Posted By JVGen
Hi Brian, I'm getting an error while trying...

Hi Brian,

I'm getting an error while trying to use tadpole. Tadpole.sh brings up the expected list of options, so I know that I've directed the terminal correctly.

However, adding the...
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