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Forum: Bioinformatics 07-31-2014, 04:28 AM
Replies: 4
Views: 1,032
Posted By hbt
That's great, thank you all

That's great, thank you all
Forum: Bioinformatics 07-31-2014, 03:41 AM
Replies: 4
Views: 1,032
Posted By hbt
Question Producing associated gene lists.......?

Does anyone know the best way to produce a list of genes (official gene ID preferably) that have the same associated function.

for example i want to get a comprehensive list of official gene IDs...
Forum: Bioinformatics 02-24-2014, 06:04 AM
Replies: 1
Views: 1,057
Posted By hbt
Question Cuffdiff 0 tests with iGenomes?...

I'm trying to run a number of data sets with the most recent version of cuffdiff.

Previously with Cufflinks 2.02 I would provide cuffdiff with the .Bam files from tophat2 (2.04) and both the...
Forum: Bioinformatics 02-05-2013, 01:22 AM
Replies: 4
Views: 1,706
Posted By hbt
Thank you, but how could I determine which SNPs...

Thank you, but how could I determine which SNPs in the resulting output file were unique to one of the input BAMs and which were common across all in-putted BAMs?
Forum: Bioinformatics 02-01-2013, 07:20 AM
Replies: 4
Views: 1,706
Posted By hbt
Anyone.........? :(

Anyone.........? :(
Forum: Bioinformatics 01-29-2013, 11:18 PM
Replies: 4
Views: 1,706
Posted By hbt
Question [B]Mpileup on multiple BAM files, common SNPs?[/B]

Does anyone know the best way to discover only the common SNPs across multiple Bam files?
Is this best achieved running each Bam individually and somehow filtering the vcf files or can it be done by...
Forum: Bioinformatics 11-09-2012, 02:20 AM
Replies: 3
Views: 4,279
Posted By hbt
Question Alternative to cufflinks? - Bam to count table?

From the numerous posts here on seqanswers it's becoming increasingly evident that cufflinks and cuffdiff have some major issues relating to calculation of DE significance across multiple samples.
...
Forum: Bioinformatics 10-10-2012, 05:48 AM
Replies: 2
Views: 2,538
Posted By hbt
Is this an issue just with the newest version of...

Is this an issue just with the newest version of cufflinks (v.2.02) or did it also occur with older versions of cufflinks?
Forum: Bioinformatics 10-08-2012, 08:06 AM
Replies: 8
Views: 2,669
Posted By hbt
We've also had problems running Tophat 2 on...

We've also had problems running Tophat 2 on multiple cores, usually it would fail at the point where multiple BAM files are merged into 1.
However we found that running on 4 cores worked so have...
Forum: Bioinformatics 05-30-2012, 02:59 AM
Replies: 4
Views: 1,724
Posted By hbt
Cufflinks doesn't "assemble" the reads it merely...

Cufflinks doesn't "assemble" the reads it merely annotates and quantifies the number of reads that map to each separate location of the genome e.g. an exon.
To view how the reads have mapped try...
Forum: Bioinformatics 05-02-2012, 01:59 AM
Replies: 1
Views: 1,630
Posted By hbt
Sorry, have re-posted in correct forum (Sample...

Sorry, have re-posted in correct forum (Sample Prep / Library Generation)
Forum: Sample Prep / Library Generation 05-02-2012, 01:57 AM
Replies: 1
Views: 2,189
Posted By hbt
Question RIN vs Volume?

I have a set of RNA samples prepared for RNAseq, however the RIN values and total volume on a few of the samples are less than ideal (<7.0 RIN and ~1.5ug total RNA) per sample

I have now produced...
Forum: Bioinformatics 05-02-2012, 01:14 AM
Replies: 1
Views: 1,630
Posted By hbt
Question RIN vs Volume?

I have a set of RNA samples prepared for RNAseq, however the RIN values and total volume on a few of the samples are less than ideal (<7.0 RIN and ~1.5ug total RNA) per sample

I have now produced...
Forum: Bioinformatics 03-13-2012, 03:51 AM
Replies: 3
Views: 2,273
Posted By hbt
Exclamation iGenomes data set....which to use?

Can anyone shed any light on the relative merits of the 3 sources of reference data available on iGenomes (UCSC/NCBI/Ensembl)?

Thanks

Huw
Forum: Bioinformatics 10-31-2011, 12:02 AM
Replies: 14
Views: 7,371
Posted By hbt
That's great thank you

That's great thank you
Forum: Bioinformatics 10-28-2011, 04:15 AM
Replies: 14
Views: 7,371
Posted By hbt
Question Venn diagram for DE data?

Does anyone know of a free software package that would allow me to produce a venn diagram based on the differential expression values obtained from a cufflinks>cuffdiff analysis? (or even using just...
Forum: Bioinformatics 10-18-2011, 02:07 AM
Replies: 17
Views: 16,125
Posted By hbt
@sdarko Could you explain little how you went...

@sdarko Could you explain little how you went about "renaming the gtf and fasta header entries so that they matched" please.
I'm keen to update the gtf I use with tophat to the ensembl version.
...
Forum: Bioinformatics 10-06-2011, 02:23 AM
Replies: 4
Views: 16,503
Posted By hbt
I'd love to know the answers to this too! ...

I'd love to know the answers to this too!

cheers
Forum: Bioinformatics 07-06-2011, 06:04 AM
Replies: 0
Views: 1,400
Posted By hbt
Question Human transcriptome reference in colour space

Does anyone know if there is a freely available human transcriptome reference in colour space out there?

Thanks

Huw
Forum: Bioinformatics 04-11-2011, 03:50 AM
Replies: 4
Views: 3,596
Posted By hbt
Unhappy Bowtie and Tophat

We are currently trying to analyse Solid RNA-seq data using tophat and/or bowtie.
With default settings tophat is able to align about 35% of reads, whereas bowtie on default is able to align 53%!!...
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