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Forum: RNA Sequencing 09-03-2012, 09:21 AM
Replies: 4
Views: 2,528
Posted By AdamB
I should have mentioned - this is when I use the...

I should have mentioned - this is when I use the -g or -G option.
Forum: RNA Sequencing 08-31-2012, 04:56 AM
Replies: 4
Views: 2,528
Posted By AdamB
XLOC identifiers from cufflinks/cuffmerge/cuffdiff

Is there a way to stop cufflinks replacing Ensembl gene IDs from the reference gtf with its own XLOC identifiers? Or is it possible to convert all the XLOCs back to Ensembl gene IDs after running...
Forum: Bioinformatics 04-13-2011, 11:07 AM
Replies: 27
Views: 9,812
Posted By AdamB
I mean there is an enrichment of reads at the...

I mean there is an enrichment of reads at the regions surrounding the TSS, relative to the rest of the genome. One sample isn't consistently increased across the whole genome, since I'm normalising...
Forum: Bioinformatics 04-11-2011, 11:23 AM
Replies: 27
Views: 9,812
Posted By AdamB
@Simon Anders Would DESeq apply linear scaling...

@Simon Anders
Would DESeq apply linear scaling between treatments (rather than between sample X and input X)? Please can you elaborate more on what you would like to see in a scatter plot? Also, are...
Forum: Bioinformatics 04-08-2011, 07:01 AM
Replies: 27
Views: 9,812
Posted By AdamB
@mudshark When you say 'difference in...

@mudshark

When you say 'difference in sequencing depth', do you mean technical variation arising somewhere between the library construction and obtaining mapped reads? Because my other point was...
Forum: Bioinformatics 04-08-2011, 03:13 AM
Replies: 7
Views: 2,063
Posted By AdamB
15. SeqMonk...

15. SeqMonk (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/)
16. Partek (http://www.partek.com/ngs)

There are loads out there!
Forum: Bioinformatics 04-08-2011, 03:10 AM
Replies: 27
Views: 9,812
Posted By AdamB
I don't believe differential histone modification...

I don't believe differential histone modification can be determined purely by comparing counts. Did you normalise your ChIP samples to input control for peak calling? There should at least be some...
Forum: Bioinformatics 04-08-2011, 02:42 AM
Replies: 2
Views: 1,830
Posted By AdamB
The current version of Cufflinks supports...

The current version of Cufflinks supports replicates for comparison.
Forum: Bioinformatics 03-31-2011, 07:48 AM
Replies: 7
Views: 1,819
Posted By AdamB
Small update: I tried to generate a wig file,...

Small update: I tried to generate a wig file, which worked apart from that the chromosome name in the header was "chr1.fa". UCSC did not like this, so I changed the chromosome name to "chr1", and...
Forum: Bioinformatics 03-31-2011, 04:19 AM
Replies: 7
Views: 1,819
Posted By AdamB
I can confirm the latest version (4.0.17)...

I can confirm the latest version (4.0.17) successfully separated my reads using the "elandext" flag.

Thanks for your help.
Forum: Bioinformatics 03-31-2011, 03:13 AM
Replies: 8
Views: 2,642
Posted By AdamB
DAVID (http://david.abcc.ncifcrf.gov/tools.jsp)...

DAVID (http://david.abcc.ncifcrf.gov/tools.jsp) is quite useful for GO analysis. Paste in your IDs, and specify what type they are.
Forum: Bioinformatics 03-25-2011, 08:22 AM
Replies: 7
Views: 1,819
Posted By AdamB
Hi Anthony, Yes I'd definitely like to try...

Hi Anthony,

Yes I'd definitely like to try compiling the latest version. Is it on the website?

Thanks
Forum: Bioinformatics 03-15-2011, 12:19 PM
Replies: 7
Views: 1,819
Posted By AdamB
FindPeaks SeparateReads.jar error using GERALD/ELAND-generated files

I'm trying to use FindPeaks with some data mapped in ELAND via GERALD. At the moment I'm stuck on using SeparateReads.jar. Below is a sample of the data from the input "s_X_sorted.txt" file:
...
Forum: Bioinformatics 02-07-2011, 03:11 AM
Replies: 2
Views: 2,000
Posted By AdamB
Hi Mike, I had this problem when mapping...

Hi Mike,

I had this problem when mapping some SOLiD data with TopHat. The unmatched reads were all reverse reads, so it was relatively straightforward to solve by sorting with the matched _2 reads...
Forum: Bioinformatics 02-03-2011, 07:53 AM
Replies: 9
Views: 6,439
Posted By AdamB
An update: I realised there are not the same...

An update:

I realised there are not the same number of F3 reads as F5-BC reads:
F3 = 23,077,379
F5-BC = 26,929,508

So, for a sample of 250,000 reads, I extracted those reads for which there...
Forum: Bioinformatics 01-31-2011, 03:54 AM
Replies: 9
Views: 6,439
Posted By AdamB
If anyone has an answer to this question it would...

If anyone has an answer to this question it would be much appreciated, thanks.
Forum: Bioinformatics 01-27-2011, 04:00 AM
Replies: 9
Views: 6,439
Posted By AdamB
Also if anyone has tips on how to extract a...

Also if anyone has tips on how to extract a subset of matching F3 and F5 reads from .csfasta and .qual files, please let me know.
Forum: Bioinformatics 01-27-2011, 03:08 AM
Replies: 9
Views: 6,439
Posted By AdamB
I have previously mapped the reads using Bioscope...

I have previously mapped the reads using Bioscope (ABI), and that gave me the mate pair distance stats. I just tried TopHat using 12550 bp, which I thought more accurately reflected the spread, but...
Forum: Bioinformatics 01-26-2011, 03:49 AM
Replies: 9
Views: 6,439
Posted By AdamB
'Properly paired' reads in sam flag from TopHat mapping

I ran TopHat on a SOLiD paired-end dataset using the following command:
tophat --color --quals --library-type fr-secondstrand -r 125 -p 7 -o /home/me/data/raw_reads/bowtie_out/sample_secstrand -G...
Forum: Bioinformatics 01-25-2011, 03:55 AM
Replies: 35
Views: 8,899
Posted By AdamB
Thanks adarob. Do you know where I can find...

Thanks adarob.

Do you know where I can find the mapping stats from the TopHat run (% mapped, % paired, etc)? I saw them in the individual logs, but not all collected in one file.

Thanks.
Forum: Bioinformatics 01-24-2011, 10:33 AM
Replies: 35
Views: 8,899
Posted By AdamB
Hi, Please can anyone who has used TopHat...

Hi,

Please can anyone who has used TopHat with SOLiD strand-specific data, say whether you used the fr-firststrand, fr-secondstarand or neither option?

To be clear, I'm using paired-end (50+25...
Forum: Bioinformatics 01-10-2011, 04:29 AM
Replies: 15
Views: 5,860
Posted By AdamB
For me, it definitely fixed the problem by adding...

For me, it definitely fixed the problem by adding "chr" to the chromosome field.
Forum: Bioinformatics 01-10-2011, 04:18 AM
Replies: 15
Views: 5,860
Posted By AdamB
@Bacilo: I'm not sure if I understrand, but...

@Bacilo:

I'm not sure if I understrand, but did you try changing the chromosome field in the Ensembl gtf to "chrX"?
Forum: Bioinformatics 12-07-2010, 06:34 AM
Replies: 15
Views: 5,860
Posted By AdamB
This worked for me when I was trying to use a gtf...

This worked for me when I was trying to use a gtf from Ensembl.
Forum: Bioinformatics 10-20-2010, 03:10 AM
Replies: 35
Views: 8,899
Posted By AdamB
Did you try feeding the output from the PE data...

Did you try feeding the output from the PE data into cufflinks? If so, did it report 50+25 bp reads?
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