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Search: Posts Made By: sudders
Forum: Bioinformatics 09-08-2017, 12:57 AM
Replies: 3
Views: 2,034
Posted By sudders
There was a bug in the release version that made...

There was a bug in the release version that made the `--set-cell-number` and `--plot-prefix` options incompatible. If you run without `--plot-prefix` (like in the TL;DR version of the guide) it...
Forum: Bioinformatics 08-22-2017, 02:03 AM
Replies: 3
Views: 2,034
Posted By sudders
UMI-Tools version 0.5: now with tools for cell barcoded scRNA-seq

We are proud to announce the release of UMI-Tools 0.5.

UMI-tools provides error aware tools for dealing with short random oligos (Unique Molecular Identifiers/Random Molecular Tags).

The novel,...
Forum: Bioinformatics 03-14-2016, 02:22 AM
Replies: 12
Views: 7,225
Posted By sudders
You've probably worked this out already, but yes,...

You've probably worked this out already, but yes, it handles splice-aware mappings.
Forum: Bioinformatics 11-23-2015, 01:30 AM
Replies: 5
Views: 4,269
Posted By sudders
I just though people might like to know that we...

I just though people might like to know that we never did get to the bottom of the baised UMI usage, but we did find an even bigger problem - PCR and sequencing errors in UMIs.

We've created some...
Forum: Bioinformatics 12-05-2014, 01:49 AM
Replies: 1
Views: 2,779
Posted By sudders
Hi, Did you ever get this sorted? I can't...

Hi,

Did you ever get this sorted? I can't seem to find any annotation of tRNAs in human ensembl.

Ian
---
Forum: Bioinformatics 05-13-2014, 08:08 AM
Replies: 5
Views: 4,269
Posted By sudders
Bias in unique molecular identifier usage

Hi All,

I'm analysing some iCLIP data generated following Koning et al, Jove 2011 (http://www.jove.com/video/2638/iclip-transcriptome-wide-mapping-protein-rna-interactions-with).

Included in...
Forum: Bioinformatics 05-07-2014, 02:29 AM
Replies: 5
Views: 1,711
Posted By sudders
No sorry, i've just given up using the provided...

No sorry, i've just given up using the provided stats on such large projects.
Forum: Bioinformatics 02-27-2014, 02:02 AM
Replies: 8
Views: 3,013
Posted By sudders
Hi Tommy, Sorry for the slow reply, i've...

Hi Tommy,

Sorry for the slow reply, i've been away. In future, if you use the CGAT user group (https://groups.google.com/forum/?fromgroups#!forum/cgat-user-group), your message will go to more...
Forum: Bioinformatics 02-03-2014, 06:03 AM
Replies: 10
Views: 4,611
Posted By sudders
I believe the the Kraken...

I believe the the Kraken (http://www.ebi.ac.uk/research/enright/software/kraken) pipeline will process miRNA-seq data into the format you require - it includes options to summarise counts per gene or...
Forum: Bioinformatics 02-01-2014, 11:04 AM
Replies: 8
Views: 3,013
Posted By sudders
Hi Tommy, Thanks for your interest. ...

Hi Tommy,

Thanks for your interest.

Simple average profiles are produced automatically by the script (using matplotlib code rather than R).

You can use R to produce more complex plots (like...
Forum: Bioinformatics 01-09-2014, 05:03 AM
Replies: 8
Views: 3,013
Posted By sudders
Sorry, should now be fixed.

Sorry, should now be fixed.
Forum: Bioinformatics 01-09-2014, 04:46 AM
Replies: 8
Views: 3,013
Posted By sudders
Introducing CGAT: computational genomics analysis toolkit

We have just published CGAT: computational genomics analysis toolkit (http://www.ncbi.nlm.nih.gov/pubmed/24395753) in Bioinformatics.

The toolkit grew out of the code base that we have developed...
Forum: Bioinformatics 10-31-2013, 05:30 AM
Replies: 3
Views: 1,654
Posted By sudders
Cheers that worked great thanks. For anyone...

Cheers that worked great thanks.

For anyone reading this in the future though should note that our 128GB server didn't have enough memory to process the whole genome in one go and it was necessary...
Forum: Bioinformatics 10-30-2013, 05:23 AM
Replies: 3
Views: 1,654
Posted By sudders
Restriction Digests with ambiguity

Hi All,

I'm trying to identify sites restriction sites in the genome. Some of the enzymes I'm using contain ambiguity, e.g. ApoI whose site is RAATTY.

Initially i've been trying to use...
Forum: Bioinformatics 10-29-2013, 09:11 AM
Replies: 1
Views: 1,852
Posted By sudders
Weird PNEXT and RNEXT values in Bam from BWA

Hi All,

I'm using BWA to align some paired end illunmina data. The reads vary in length, but around 45-50bp. I fully expect that a large portion of reads will not pair nicely.

I run BWA aln on...
Forum: Bioinformatics 11-28-2012, 02:22 AM
Replies: 1
Views: 1,401
Posted By sudders
Hi, I've done this using DEXSeq, I just used...

Hi, I've done this using DEXSeq, I just used DEXSeq and treated the junciton counts as exon counts and then did DEXSeq as usual.

I found that the results as WAY more conservative than DEXSeq on...
Forum: Bioinformatics 10-10-2012, 12:37 AM
Replies: 2
Views: 1,855
Posted By sudders
We've noticed this as well. BWA seems to give a...

We've noticed this as well. BWA seems to give a position to unaligned reads.
Forum: RNA Sequencing 10-10-2012, 12:21 AM
Replies: 47
Views: 45,996
Posted By sudders
As far as I can see you have two alternatives...

As far as I can see you have two alternatives here. First you could use some kind of alignment to match the contigs across samples. Maybe best reciprical blast hits? A second alternative would be...
Forum: Bioinformatics 09-11-2012, 09:44 AM
Replies: 21
Views: 4,723
Posted By sudders
We've been seeing this for quite a while now....

We've been seeing this for quite a while now. There is another thread about this here: http://seqanswers.com/forums/showthread.php?t=16962

There was some claim that using 2.0.2 fixed this,...
Forum: Bioinformatics 09-10-2012, 06:50 AM
Replies: 5
Views: 1,711
Posted By sudders
Yes, exactly. One would normally expect to...

Yes, exactly.

One would normally expect to see a whole load of stats about the run,

something like:

# Cuffcompare v2.0.2 | Command line was:
#cuffcompare -o tax-Pre-agg.cuffcompare -s...
Forum: Bioinformatics 09-10-2012, 01:55 AM
Replies: 5
Views: 1,711
Posted By sudders
no cuffcompare .stats with more than 6 samples

Hi All,

I'm having a weird issue with the output from cuffcompare, and I wondered if anyone had seen the same.

We are using cuffcompare to comapre and track transcripts build from an RNAseq...
Forum: Bioinformatics 08-08-2012, 11:45 PM
Replies: 10
Views: 10,011
Posted By sudders
I've been using cutadapt with more success.

I've been using cutadapt with more success.
Forum: Bioinformatics 05-30-2012, 04:41 AM
Replies: 46
Views: 19,762
Posted By sudders
We eventually came to the conclusion that the...

We eventually came to the conclusion that the original problem in Cufflinks 1.3 was being caused by excessive variance between our samples. As more samples were added, the variance was getting bigger...
Forum: Bioinformatics 05-22-2012, 09:33 AM
Replies: 10
Views: 10,011
Posted By sudders
Hi, I've also had problems with fastx...

Hi,

I've also had problems with fastx clipper. Its seems that not only is it not doing the trimming I expect, but some thing is also a bit odd about what it outputs.


I tested this by passing...
Forum: Bioinformatics 04-27-2012, 05:52 AM
Replies: 10
Views: 6,998
Posted By sudders
You could in theory divide the input bams by...

You could in theory divide the input bams by which chromosomes the reads map to and then run a seperate cufflinks process for each chromosome. You'd have to find some way to renormalise the FPKMs...
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