SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 14 of 14
Search took 0.02 seconds.
Search: Posts Made By: flipwell
Forum: Bioinformatics 09-03-2013, 04:46 PM
Replies: 3
Views: 1,555
Posted By flipwell
Has anyone had any trouble running this script?...

Has anyone had any trouble running this script? When I try to run it nothing happens. I don't get any errors it just seems to sit there and produce nothing. Does it take a long time to run?

Thanks
Forum: Bioinformatics 09-09-2012, 09:35 PM
Replies: 6
Views: 3,824
Posted By flipwell
Just wondering if you found out anything more...

Just wondering if you found out anything more about this issue as the data I am currently working on is giving the same result following BWA assembly.

Thanks
Forum: Bioinformatics 05-21-2012, 05:02 PM
Replies: 3
Views: 2,834
Posted By flipwell
No I ended up just running it without trimming as...

No I ended up just running it without trimming as I decided it wasn't really necessary
Forum: Bioinformatics 09-05-2011, 06:49 PM
Replies: 6
Views: 5,025
Posted By flipwell
OrthoMCL duplicate entry error

I have made it up to step 10 of the orthomcl process, finding protein pairs, but have become stuck with a duplicate entry error:

Duplicate entry '5206|CNAG_00003-5206|CNE00390' for key...
Forum: Bioinformatics 08-23-2011, 09:01 PM
Replies: 10
Views: 9,063
Posted By flipwell
I have run it and got a few of those errors. It...

I have run it and got a few of those errors. It still completed though and I've compared the results with what I found with BreakDancer - didn't find anything new, BreakDancer picked up around 80%...
Forum: Bioinformatics 08-17-2011, 04:48 PM
Replies: 5
Views: 3,193
Posted By flipwell
I found it was because I hadn't given the...

I found it was because I hadn't given the -species option, works fine now
Forum: Bioinformatics 08-15-2011, 05:48 PM
Replies: 2
Views: 3,119
Posted By flipwell
Thank you so much! I completely missed that...

Thank you so much! I completely missed that folder when I extracted and just assumed it was part of Tree.
Forum: Bioinformatics 08-14-2011, 07:31 PM
Replies: 2
Views: 3,119
Posted By flipwell
CREST/perl module Tree::Interval

I'm trying to run CREST (http://www.stjuderesearch.org/site/lab/zhang) but it is trying to locate a perl module Tree::Interval which I have had no luck finding anywhere. Does anyone know where I can...
Forum: Genomic Resequencing 07-10-2011, 03:22 PM
Replies: 27
Views: 17,436
Posted By flipwell
Did you try FreeBayes? I'm facing this problem...

Did you try FreeBayes? I'm facing this problem now and wondering what to use. I've tried GATK and it does appear to work (very superficial examination) but am concerned there might be issues I'm...
Forum: Bioinformatics 04-19-2011, 08:03 PM
Replies: 6
Views: 3,960
Posted By flipwell
I have had this error a couple of times as well...

I have had this error a couple of times as well and found that if I reran sampe/samse and tried to convert again then it was fine
Forum: Bioinformatics 04-11-2011, 04:46 PM
Replies: 9
Views: 2,836
Posted By flipwell
I haven't tried it, but during SNP detection you...

I haven't tried it, but during SNP detection you can select to annotate the consensus with SNPs or not - if you choose vote for ambiguities during alignment then annotate with SNPs during detection...
Forum: Bioinformatics 04-10-2011, 09:26 PM
Replies: 5
Views: 3,193
Posted By flipwell
Thanks for your reply - I can't find a *.log2...

Thanks for your reply - I can't find a *.log2 file either

I ran it as follows: RepeatMasker ../../H99index/H99+mito.fa -lib output_repeats.fa
Then I added the -dir . and some extra output...
Forum: Bioinformatics 04-10-2011, 08:15 PM
Replies: 5
Views: 3,193
Posted By flipwell
RepeatMasker output

Where is the output from RepeatMasker saved? I can see the temporary folder in my directory during running but it disappears when it finishes and I can't find a *.masked file anywhere! Is there a...
Forum: Bioinformatics 04-01-2011, 07:17 PM
Replies: 3
Views: 2,834
Posted By flipwell
BWA errors after quality trimming

After I use the "-q 20" option in bwa aln I start getting errors down the road eg when i run ValidateSamFile in picard I get lots of "Mate negative strand flag does not match read negative strand...
Showing results 1 to 14 of 14

 


All times are GMT -8. The time now is 09:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO