SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 31
Search took 0.00 seconds.
Search: Posts Made By: Greg
Forum: Bioinformatics 04-04-2018, 10:27 AM
Replies: 5
Views: 3,689
Posted By Greg
Okay cool, thanks for the quick response!

Okay cool, thanks for the quick response!
Forum: Bioinformatics 04-04-2018, 09:46 AM
Replies: 5
Views: 3,689
Posted By Greg
bbmap callvariants.sh multisample vcf format, wrong number of fields

Trying to use BBMap callvariants on multiple samples. The resulting VCF does not have the sample names and yields an error with any vcf tools:


vcf-validator tmp.vcf
Wrong number of fieldsin...
Forum: Illumina/Solexa 11-26-2014, 03:51 PM
Replies: 6
Views: 3,726
Posted By Greg
Very cool. I'd be happy to annotate/maintain a...

Very cool. I'd be happy to annotate/maintain a list or spreadsheet as a resource if people want to contribute. There is one in my building I can add!
HighSeq 2000: HWI-ST765
Forum: Illumina/Solexa 11-26-2014, 03:03 PM
Replies: 6
Views: 3,726
Posted By Greg
Great! ...can you give me an idea how?

Great! ...can you give me an idea how?
Forum: Illumina/Solexa 11-26-2014, 01:26 PM
Replies: 6
Views: 3,726
Posted By Greg
Can I get the Illumina model from a machines name?

Hi All,
I understand that the header in Illumina Fastq files contains the name of the machine that carried out the sequencing. Is it possible to figure out what model the machine was (GAII vs...
Forum: Bioinformatics 01-01-2014, 12:08 PM
Replies: 8
Views: 3,884
Posted By Greg
In getting examples ready for you I realized I...

In getting examples ready for you I realized I made an embarrassingly simple error. Your script works great. Thanks again! Happy new year.
Forum: Bioinformatics 01-01-2014, 11:50 AM
Replies: 8
Views: 3,884
Posted By Greg
dpryan, I successfully compiled and ran your...

dpryan, I successfully compiled and ran your program. Unfortunately, as far as I can tell the resulting bam files are no longer indexed and I think have also been stripped of the read group header...
Forum: Bioinformatics 01-01-2014, 10:18 AM
Replies: 8
Views: 3,884
Posted By Greg
Wow, awesome. This is exactly what I was hoping...

Wow, awesome. This is exactly what I was hoping for. I will give it a try right away and let you know how it goes.
Forum: Bioinformatics 12-31-2013, 07:07 PM
Replies: 8
Views: 3,884
Posted By Greg
Thanks Zapages, Looks like a do-able work...

Thanks Zapages,
Looks like a do-able work around BUT i would like to avoid uploading data to galaxy if possible...
Forum: Bioinformatics 12-31-2013, 06:02 PM
Replies: 8
Views: 3,884
Posted By Greg
BAM quality how to convert illumina 1.5 to 1.9?

Welcoming 2014 the best way I know...

I've aligned a good deal of illumina data I have accumulated in order to call SNPs with GATK. I had over looked the fact that some of the older runs are with...
Forum: Bioinformatics 10-22-2010, 10:18 AM
Replies: 2
Views: 2,570
Posted By Greg
Not even a nibble?

Not even a nibble?
Forum: Bioinformatics 10-20-2010, 12:41 PM
Replies: 2
Views: 2,570
Posted By Greg
alternative splicing quantification and comparison with RNAseq

As there is no consensus in the literature on this I thought it might be worth it to try to generate some discussion here. I am interested in finding quantitative changes in alternative splicing (AS)...
Forum: Bioinformatics 07-19-2010, 11:14 AM
Replies: 366
Views: 222,965
Posted By Greg
This is a really awesome program. I really like...

This is a really awesome program. I really like how easy it is to use and how clearly it summarizes everything.

One thing, I cant seem to copy and paste out overrepresented sequences. This would...
Forum: Bioinformatics 07-16-2010, 02:59 PM
Replies: 0
Views: 1,351
Posted By Greg
Missing partners - tophat and paired ends

With and without mismatches I find that some (up to 1/3) of my paired end reads only have one of the two mates align.

So, how does tophat deal with paired ends?

How might this affect...
Forum: Bioinformatics 07-15-2010, 10:41 AM
Replies: 5
Views: 5,617
Posted By Greg
I've had the same experience. Could only guess...

I've had the same experience. Could only guess...
Forum: Bioinformatics 07-09-2010, 03:58 PM
Replies: 0
Views: 1,803
Posted By Greg
Can you spot whats wrong with this .gff3?

Hello,
I've been working with tophat for a while pretty successfully, but for some reason this one data set will not cooperate. Using the .gff file I downloaded for the corresponding genome I get:
...
Forum: Bioinformatics 07-05-2010, 11:12 AM
Replies: 1
Views: 2,255
Posted By Greg
Is there anyway to do this? Cuffdiff is a great...

Is there anyway to do this? Cuffdiff is a great tool and it would especially useful for this project. Maybe I should clarify that the distance between the mate pairs is what is different within and...
Forum: Bioinformatics 06-30-2010, 06:14 PM
Replies: 5
Views: 5,617
Posted By Greg
So I just found the -c option to set the number...

So I just found the -c option to set the number of required reads. It does change the number of tests that happen but there are still less then I would think. Any ideas? What are the other criteria...
Forum: Bioinformatics 06-29-2010, 02:48 PM
Replies: 1
Views: 2,255
Posted By Greg
paired ends with cuffdiff

Whats the best way to deal with paired end reads of different lengths when using cuffdiff? I have multiple runs at different lengths for the same treatment that I want to compare to another...
Forum: Bioinformatics 06-28-2010, 03:35 PM
Replies: 5
Views: 5,617
Posted By Greg
Cuffdiff NOTEST for splicing.diff

Using the tophat/cufflinks combo to find differential alternative splicing.

The cuffdiff manual says that if there "not enough alignments for testing" then you will get NOTEST and the treatments...
Forum: Bioinformatics 06-25-2010, 04:11 PM
Replies: 0
Views: 2,806
Posted By Greg
gff and gff3 formating fun

Is it just me or does flybase only have .gff files for all the drosophila species and not .gff3 or gtf? Whats the best way/is it possible to convert from .gff to gff3?

thanks
Forum: Bioinformatics 06-25-2010, 10:49 AM
Replies: 3
Views: 5,979
Posted By Greg
Multimapping reads are definitely an issue....

Multimapping reads are definitely an issue. Tophat/bowtie will filter these for you if you set -g to 1. I think there are some papers that use some kind of likelyhood approach to assign ambiguous...
Forum: Bioinformatics 06-24-2010, 11:33 AM
Replies: 1
Views: 4,241
Posted By Greg
Cuffdiff splicing.diff

Hello everyone,

I just want to clarify the differences between two of the cuffdiff output files, splicing.diff and isoform_exp.diff. Splicing.diff tests whether or not the relative contribution of...
Forum: Bioinformatics 04-05-2010, 11:57 AM
Replies: 1
Views: 1,311
Posted By Greg
Am I missing something obvious or is everyone...

Am I missing something obvious or is everyone else as baffled as me?
Forum: Bioinformatics 04-03-2010, 10:56 AM
Replies: 1
Views: 1,311
Posted By Greg
Tophat oddness

I've been using tophat with some success until recently. I have one data set that seems to me to be the exact same as my other files, in the same format etc (I even changed the name lines to match...
Showing results 1 to 25 of 31

 


All times are GMT -8. The time now is 03:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO