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Forum: Bioinformatics 03-01-2018, 01:36 PM
Replies: 0
Views: 327
Posted By hepcat72
Quick & dirty DNA coordinates in any mac app

I just wrote 3 Automator services on my mac that help me with the debugging of DNA modification scripts I've been writing. Of course, there are other ways to do it. I kinda just did it for fun,...
Forum: General 07-26-2017, 03:38 PM
Replies: 1
Views: 917
Posted By hepcat72
The answer is, the presence or absence of 'X' in...

The answer is, the presence or absence of 'X' in a protein weight matrix should not affect the alignment of sequences not containing 'X', however there is a bug in muscle that is fixed by the...
Forum: General 07-18-2017, 07:51 AM
Replies: 1
Views: 917
Posted By hepcat72
How do matrix weights for amino acid 'X' affect protein alignments in MUSCLE?

Sorry, this is a cross-post from biostars, but I haven't had any luck there in figuring this out...

I'm developing a protein weight matrix from scratch to use with MUSCLE. I started with the 20...
Forum: Bioinformatics 04-07-2014, 06:41 AM
Replies: 7
Views: 2,010
Posted By hepcat72
Same problem

I too am trying to compile an hg19 ublast database and have encountered the same error. I just checked for carriage returns in the hg19.fa file and there are none. Yet I get the error:

---Fatal...
Forum: Bioinformatics 04-26-2011, 07:49 AM
Replies: 26
Views: 12,068
Posted By hepcat72
I sorted the file using `samtools sort`. I...

I sorted the file using `samtools sort`. I indexed it as well. Still no luck. My output files, aside from the headers, are empty. breakdancer_max complains about missing LB tags in the @RG header...
Forum: Bioinformatics 04-26-2011, 06:20 AM
Replies: 26
Views: 12,068
Posted By hepcat72
I sorted via MosaikSort which was then converted...

I sorted via MosaikSort which was then converted to bam. I'm running another attempt right now after a sort attempt with `samtools sort`. I'll try an index next if that doesn't work. Do I have to...
Forum: Bioinformatics 04-25-2011, 12:14 PM
Replies: 26
Views: 12,068
Posted By hepcat72
I'm having the same problem. I get a cfg file...

I'm having the same problem. I get a cfg file that looks fine, but only the header comes out of BreakDancerMax. I know that the data should have SVs in it because it's from a published paper about...
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