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Search: Posts Made By: hlwright
Forum: Bioinformatics 01-22-2013, 06:57 AM
Replies: 3
Views: 3,187
Posted By hlwright
Postscript to my last message, I think the...

Postscript to my last message, I think the crashing may be a Mac OS problem, as I have managed to run edgeR on a small dataset on a Windows machine, plus MeV crashes on the Mac using the supplied...
Forum: Bioinformatics 01-22-2013, 06:26 AM
Replies: 3
Views: 3,187
Posted By hlwright
Hi Simon Thanks for replying so quickly....

Hi Simon

Thanks for replying so quickly. Having struggled over this for 2 weeks I think I have now managed to work it out by myself (the power of posting on SeqAnswers!). I didn't have all the...
Forum: Bioinformatics 01-22-2013, 04:54 AM
Replies: 3
Views: 3,187
Posted By hlwright
RNA-Seq analysis using MeV

I have an Excel file (tab delimited .txt) of count data generated using htseq which I am trying to upload into MeV for RNA-Seq analysis using

File - Load Data - Select File Loader - RNASeq...
Forum: Bioinformatics 11-09-2012, 10:37 AM
Replies: 18
Views: 26,199
Posted By hlwright
dpryan - that worked brilliantly, thanks! :o)

dpryan - that worked brilliantly, thanks!

:o)
Forum: Bioinformatics 11-09-2012, 07:23 AM
Replies: 18
Views: 26,199
Posted By hlwright
Hi I have EXACTLY the same question. Does...

Hi

I have EXACTLY the same question. Does htseq take BAM files, or do you have to convert to SAM first (don't want to do this if I don't have to)?

Thanks
Forum: Bioinformatics 11-09-2012, 03:51 AM
Replies: 3
Views: 6,245
Posted By hlwright
Thanks sdriscoll - I have been getting more and...

Thanks sdriscoll - I have been getting more and more frustrated with cufflinks / cuffdiff so will explore these other options.

Really appreciate you replying to my post.

Helen
Forum: Bioinformatics 11-08-2012, 02:10 AM
Replies: 3
Views: 5,272
Posted By hlwright
Yes, we have been experiencing similar problems...

Yes, we have been experiencing similar problems (along with other problems) with the latest version of Cufflinks and are considering other methods for our DE analysis. I have some variance in my...
Forum: Bioinformatics 10-11-2012, 07:13 AM
Replies: 8
Views: 3,813
Posted By hlwright
Xiaoyu Yes I have a different number of...

Xiaoyu

Yes I have a different number of replicates when I run the analysis the second time, so I might expect that the gene RPKM value in the genes.fpkm_tracking file (one RPKM for each...
Forum: Bioinformatics 10-10-2012, 11:54 PM
Replies: 8
Views: 3,813
Posted By hlwright
I have noticied this as well. I also notice that...

I have noticied this as well. I also notice that in the new version of cufflinks (2.0.2), cuffdiff produces a file with the individual RPKM values for replicates. I have 14 disease samples and 6...
Forum: Bioinformatics 10-08-2012, 04:13 AM
Replies: 2
Views: 2,534
Posted By hlwright
Question Cufflinks timing out - computing power required?

I am analysing human transcriptome data (Illumina) via the Tophat -> Cufflinks pipeline (v2.0.2) using iGenomes references. My dataset comprises 14 patients and 6 controls, so I have 2 "conditions"...
Forum: Bioinformatics 09-13-2012, 06:56 AM
Replies: 1
Views: 1,893
Posted By hlwright
Tophat v2.0.4 memory usage

I have a question about memory use by the new version of Tophat (v2.0.4). We ran the previous versions of Tophat on our cluster over 8 threads with 2 GB RAM per thread (16 GB total) with no...
Forum: Bioinformatics 07-16-2012, 02:23 AM
Replies: 3
Views: 6,245
Posted By hlwright
Question Different RPKM values in same dataset using Cufflinks or Cuffdiff (v1.3.0)

I have generated RPKM values for the same dataset using Cufflinks (single input BAM file) and using Cuffdiff where my datasert is part of a larger set of samples (multiple input BAM files). The...
Forum: Bioinformatics 11-30-2011, 07:08 AM
Replies: 1
Views: 2,779
Posted By hlwright
Just to let everyone know I have had a pm from...

Just to let everyone know I have had a pm from Cole Trapnell and my problem is being caused by a bug in the current version of Cufflinks.

This option corrects the RPKM values:
--max-bundle-frags...
Forum: Bioinformatics 11-30-2011, 12:30 AM
Replies: 1
Views: 2,779
Posted By hlwright
Cufflinks v 1.2.0 high number of RPKM 0

I have three SOLiD human RNA-Seq libraries which I am analysing using cuffdiff. The libraries have a large number of reads which MAY be pcr duplicates (~90%), but as they are single-end reads I have...
Forum: Bioinformatics 10-10-2011, 11:36 PM
Replies: 6
Views: 7,627
Posted By hlwright
Thanks Chipper, your advice has solved the...

Thanks Chipper, your advice has solved the problem.

For anyone else who may be having the same problem, here is the solution:-

Create a sequence dictionary for your reference.fa in the same...
Forum: Bioinformatics 10-10-2011, 10:51 PM
Replies: 6
Views: 7,627
Posted By hlwright
Chipper - thank you. I will try your suggestion...

Chipper - thank you. I will try your suggestion today.

Jon - We run Bowtie using best and strata settings, and trim the 3' end of the read, which as far as I am aware you cannot do using TopHat. ...
Forum: Bioinformatics 10-10-2011, 02:15 AM
Replies: 6
Views: 7,627
Posted By hlwright
Here are the headers: Tophat output before...

Here are the headers:

Tophat output before Picard sorting:
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:249250621
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895...
Forum: Bioinformatics 10-10-2011, 01:05 AM
Replies: 6
Views: 7,627
Posted By hlwright
Question Problem merging BAM files

Hi everyone. We are having difficulty merging BAM files. Our pipeline so far is this:-

50bp single-end rna-seq reads - map to hg19 with Bowtie, writing unaligned reads to a new file and writing...
Forum: Bioinformatics 09-04-2011, 11:28 PM
Replies: 7
Views: 10,671
Posted By hlwright
I have changed the read names as suggested and...

I have changed the read names as suggested and re-run picard, but am still not happy that it has worked properly.

I also included an extra command in the command line...
Forum: Bioinformatics 09-01-2011, 10:49 AM
Replies: 7
Views: 10,671
Posted By hlwright
Thank you for the reply, I will try your...

Thank you for the reply, I will try your suggestion of changing the read names.

I have tried samtools rmdup but it removes >90% of my reads (as duplicates). :eek: I was hoping for a 'second...
Forum: Bioinformatics 09-01-2011, 01:14 AM
Replies: 7
Views: 10,671
Posted By hlwright
Picard Mark Duplicates help please

I am tying to use Picard MarkDuplicates to remove my pcr duplicates from a human rna-seq bam file. The run was paired-end but I only have about 30% properly paired (that is another story).

My...
Forum: Bioinformatics 07-14-2011, 07:33 AM
Replies: 4
Views: 3,109
Posted By hlwright
TopHat PE data not mapped in pairs - new version of TopHat

Could you please tell me if this command is still the same using the new version of TopHat (v1.3.1)?

I ask because we are trying to map SOLiD paired-end RNA-seq reads to the human genome. We are...
Forum: Bioinformatics 07-13-2011, 06:13 AM
Replies: 6
Views: 2,570
Posted By hlwright
Hi have you tried the sort function as...

Hi
have you tried the sort function as described in the cufflinks manual?

"The SAM file supplied to Cufflinks must be sorted by reference position. If you aligned your reads with TopHat, your...
Forum: SOLiD 06-27-2011, 05:10 AM
Replies: 5
Views: 3,897
Posted By hlwright
Thank you nilshomer, that link was very helpful. ...

Thank you nilshomer, that link was very helpful.

I have since found this paragraph in the Bowtie manual (http://bowtie-bio.sourceforge.net/manual.shtml):-



Thank you everyone for your help,...
Forum: SOLiD 06-24-2011, 05:25 AM
Replies: 5
Views: 3,897
Posted By hlwright
Reply to Chipper Thank you for your...

Reply to Chipper

Thank you for your response. We may indeed be getting confused with the colourspace QV. In fact we have been trying to find an explanation of how the colourspace QV relate to...
Showing results 1 to 25 of 31

 


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