SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 13 of 13
Search took 0.00 seconds.
Search: Posts Made By: SHeaph
Forum: Bioinformatics 01-11-2016, 01:37 AM
Replies: 4
Views: 2,112
Posted By SHeaph
Thanks for the suggestion. I'm performing...

Thanks for the suggestion. I'm performing multiple sequence alignments with large data sets >50,000 sequences and hoping to identify stop codon reassignments. However all three stop codons are...
Forum: Bioinformatics 01-10-2016, 10:15 AM
Replies: 4
Views: 2,112
Posted By SHeaph
Genetic Code Alteration - blastx

Hi All,

I'm not sure if I'm in the right forum with this query. But any info would be great!

I am running blastx on a standalone version of blast-2.2.31+. Using the standard genetic code each...
Forum: Bioinformatics 02-02-2013, 06:42 AM
Replies: 0
Views: 832
Posted By SHeaph
Merging files with Cuffmerge

Hi,

Can somebody please advise how the Cufflinks output files are merged together with Cuffmerge?

Does the command pool the data into the merged.gtf file?

I am comparing two conditions and...
Forum: Bioinformatics 01-31-2013, 09:06 AM
Replies: 1
Views: 1,161
Posted By SHeaph
cummeRbund analysis - genes & CDS

Hi All,

I produced the following table from a large data set using cufflinks-cuffmerge-cuffdiff. I produced a heatmap with cummeRbund based on the most significant differentially expressed genes...
Forum: Bioinformatics 01-18-2013, 07:58 AM
Replies: 8
Views: 10,974
Posted By SHeaph
That's great! Thanks for your help. Stephen

That's great! Thanks for your help.

Stephen
Forum: Bioinformatics 01-18-2013, 06:19 AM
Replies: 8
Views: 10,974
Posted By SHeaph
Hi cpleis, I was just wondering if you were...

Hi cpleis,

I was just wondering if you were able to resolve this issue? I am having similar difficulties at the moment, I have just over 200 hits and the gene ID label is also blurred. I am new to...
Forum: Bioinformatics 01-17-2013, 07:56 AM
Replies: 0
Views: 1,528
Posted By SHeaph
Creating Gene Sets - CummeRbund

Hi,

Can someone please advise me on this CummeRbund issue?

When creating a Gene Set in cummeRbund with the following:

> data(sampleData)
> myGeneIds <- sampleIDs
> myGeneIds
Forum: Bioinformatics 01-10-2013, 05:05 AM
Replies: 0
Views: 946
Posted By SHeaph
Cuffmerge Issue

Hi,

Can somebody please help/advise with this cuffmerge issue?

I am having an issue with merging the cufflinks transcripts.gtf file with cuffmerge. I have two files that I need to merge, the...
Forum: Bioinformatics 11-28-2012, 07:34 AM
Replies: 4
Views: 4,275
Posted By SHeaph
Bowtie2 Local Alignment Mode

Hi,

Can someone please advise on the below taken from the Bowtie2 manual?

When the --local option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might "trim" or...
Forum: Bioinformatics 11-27-2012, 06:40 AM
Replies: 2
Views: 2,662
Posted By SHeaph
Tophat2: Ensembl GRCh37 V's UCSC hg19

Hi,

I am new to tophat and I would like to know if there is any difference in using the bt2 index files and FASTA file from either Ensembl GRCh37 or UCSC hg19?

Are they the same files?
...
Forum: Bioinformatics 11-20-2012, 12:25 PM
Replies: 5
Views: 2,214
Posted By SHeaph
I was using a cDNA and non-coding RNA library to...

I was using a cDNA and non-coding RNA library to map the reads against. Can I use this as a GTF? if so would any unmapped reads here then be mapped against the actual genome?

Much appreciated.
Forum: Bioinformatics 11-20-2012, 12:13 PM
Replies: 5
Views: 2,214
Posted By SHeaph
Thanks for yer help

Thanks for yer help
Forum: Bioinformatics 11-20-2012, 06:52 AM
Replies: 5
Views: 2,214
Posted By SHeaph
Tophat2 Alignment Rate

Hi,

I am new to Tophat and I have an alignment rate query.

I am trying to map RNASeq paired reads (100bp) to a reference genome using Tophat (v2.0.6) and I am returning an alignment rate of...
Showing results 1 to 13 of 13

 


All times are GMT -8. The time now is 12:10 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO