Forum: Bioinformatics
02-28-2017, 06:15 AM
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Replies: 104
Views: 41,776
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...
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Forum: Bioinformatics
02-03-2017, 09:03 AM
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Replies: 104
Views: 41,776
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...
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Forum: Bioinformatics
01-17-2017, 03:46 PM
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Replies: 104
Views: 41,776
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...
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Forum: Bioinformatics
01-17-2017, 01:58 PM
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Replies: 104
Views: 41,776
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...
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Forum: Bioinformatics
01-17-2017, 12:52 PM
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Replies: 104
Views: 41,776
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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