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Search: Posts Made By: gntc
Forum: Bioinformatics 04-12-2017, 05:17 PM
Replies: 0
Views: 1,073
Posted By gntc
Methods for comparing two GWAS from different phenotypes

I'm trying to see whether there are any established methods for comparing GWAS results from two different phenotypes. I essentially want a statistical test that tests how similar the two sets of...
Forum: Bioinformatics 10-28-2016, 12:25 PM
Replies: 0
Views: 1,188
Posted By gntc
Gene Based Tests

I'm looking for a tool or set of tools that can provide gene based scores for a single individual. I'm looking to get information like number of SNPs, number of predicted deleterious variants,...
Forum: Bioinformatics 05-02-2012, 11:48 AM
Replies: 514
Views: 223,145
Posted By gntc
Duplicate outputs

I have some reads that were reported to map to hg19 uniquely (only one place in the genome) but they have two lines of output. The two lines are completely identical. This happened for many reads. ...
Forum: Bioinformatics 01-03-2012, 01:25 PM
Replies: 7
Views: 12,971
Posted By gntc
Try higher I guess. 200 worked for me when...

Try higher I guess. 200 worked for me when working with non-paired end data.
Forum: Bioinformatics 01-03-2012, 01:06 PM
Replies: 7
Views: 12,971
Posted By gntc
Yes, I believe you are running out of memory. If...

Yes, I believe you are running out of memory. If you use --chunkmbs 200 you should stop getting the warning. This may help improve your alignment statistics.
Forum: Bioinformatics 11-23-2011, 09:21 AM
Replies: 66
Views: 29,071
Posted By gntc
Does anyone know why when running One Sample Peak...

Does anyone know why when running One Sample Peak Calling Peak Detection with Boundary Refinement and Single Strand Filtering selected no .cod file is created? When I run this with my data I get 6...
Forum: Bioinformatics 11-23-2011, 09:17 AM
Replies: 66
Views: 29,071
Posted By gntc
Haha, yes dear. The windows version is buggy...

Haha, yes dear.

The windows version is buggy and annoying. Good to know that I'm not the only one doing what I'm doing and having problems with the windows version.
Forum: Bioinformatics 11-21-2011, 11:02 AM
Replies: 66
Views: 29,071
Posted By gntc
Honey, You can convert like this: BAM...

Honey,

You can convert like this:

BAM -> BED -> ALN

Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert...
Forum: Bioinformatics 11-07-2011, 01:12 PM
Replies: 66
Views: 29,071
Posted By gntc
Try reading the manual.

Try reading the manual.
Forum: Bioinformatics 11-07-2011, 10:13 AM
Replies: 66
Views: 29,071
Posted By gntc
Harishrk, What are you trying to do exactly?...

Harishrk,

What are you trying to do exactly?

First, when the command box flashes and disappears it means there was an error. Cisgenome doesn't say what the error was, it just terminates the...
Forum: Bioinformatics 10-19-2011, 10:40 AM
Replies: 13
Views: 5,540
Posted By gntc
cisgenome complaints

I have found using Cisgenome to be a very unpleasant experience. The Users Manual is very brief and often does not explain clearly how to use each program, what the program is doing, and what the...
Forum: Bioinformatics 06-29-2011, 02:59 PM
Replies: 66
Views: 29,071
Posted By gntc
missing files

Hello,

I am having trouble with CisGenome. Whenever I try to do anything that involves generating a file the file never appears. I have changed the .ini file. CisGenome is in a path that has no...
Forum: Bioinformatics 06-27-2011, 12:08 PM
Replies: 2
Views: 2,001
Posted By gntc
Identifying repeat elements

Were you ever able to find a fast, efficient method of analyzing large amounts of data? I have 15 million sequence and I would like to know what percentage of them are satellite DNA, LINEs, SINEs,...
Forum: Bioinformatics 04-04-2011, 10:34 AM
Replies: 514
Views: 223,145
Posted By gntc
mismatches

Bowtie does this automatically. The tag is XA:i:0 (for a read with 0 mismatches).
Forum: Bioinformatics 03-30-2011, 11:09 AM
Replies: 514
Views: 223,145
Posted By gntc
repeats

The files in chromFa.tar.gz each start out with a large number of 'N's. Is this due to uncertainty near the ends of chromosomes in sequencing?
Forum: Bioinformatics 03-25-2011, 04:28 PM
Replies: 514
Views: 223,145
Posted By gntc
Repeats

Does the hg19 index mask repeats in the genome?

I have illumina data that has a large number of repeats. The sequences have been mapped using ELAND and found that ~30% had >10 matches. When...
Forum: Bioinformatics 02-04-2011, 10:28 AM
Replies: 514
Views: 223,145
Posted By gntc
hg19 and allocation issues

I am new to bowtie and I am having a couple problems. First, I downloaded the hg19 ebwt files and attempted to transfer them to the server where I will be running bowtie but received errors for 5 of...
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