Forum: Bioinformatics
09-08-2017, 01:57 AM
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Replies: 3
Views: 2,155
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Forum: Bioinformatics
08-22-2017, 03:03 AM
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Replies: 3
Views: 2,155
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Forum: Bioinformatics
03-14-2016, 03:22 AM
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Replies: 12
Views: 7,407
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Forum: Bioinformatics
11-23-2015, 02:30 AM
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Replies: 5
Views: 4,340
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Forum: Bioinformatics
12-05-2014, 02:49 AM
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Replies: 1
Views: 2,876
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Forum: Bioinformatics
05-13-2014, 09:08 AM
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Replies: 5
Views: 4,340
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...
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Forum: Bioinformatics
05-07-2014, 03:29 AM
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Replies: 5
Views: 1,760
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Forum: Bioinformatics
02-27-2014, 03:02 AM
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Replies: 8
Views: 3,073
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...
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Forum: Bioinformatics
02-03-2014, 07:03 AM
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Replies: 10
Views: 4,740
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...
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Forum: Bioinformatics
02-01-2014, 12:04 PM
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Replies: 8
Views: 3,073
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...
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Forum: Bioinformatics
01-09-2014, 06:03 AM
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Replies: 8
Views: 3,073
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Forum: Bioinformatics
01-09-2014, 05:46 AM
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Replies: 8
Views: 3,073
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Forum: Bioinformatics
10-31-2013, 06:30 AM
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Replies: 3
Views: 1,685
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...
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Forum: Bioinformatics
10-30-2013, 06:23 AM
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Replies: 3
Views: 1,685
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...
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Forum: Bioinformatics
10-29-2013, 10:11 AM
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Replies: 1
Views: 1,910
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...
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Forum: Bioinformatics
11-28-2012, 03:22 AM
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Replies: 1
Views: 1,450
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...
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Forum: Bioinformatics
10-10-2012, 01:37 AM
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Replies: 2
Views: 1,906
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Forum: RNA Sequencing
10-10-2012, 01:21 AM
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Replies: 47
Views: 46,448
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...
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Forum: Bioinformatics
09-11-2012, 10:44 AM
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Replies: 21
Views: 4,836
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,...
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Forum: Bioinformatics
09-10-2012, 07:50 AM
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Replies: 5
Views: 1,760
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...
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Forum: Bioinformatics
09-10-2012, 02:55 AM
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Replies: 5
Views: 1,760
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...
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Forum: Bioinformatics
08-09-2012, 12:45 AM
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Replies: 10
Views: 10,107
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Forum: Bioinformatics
05-30-2012, 05:41 AM
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Replies: 46
Views: 20,054
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...
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Forum: Bioinformatics
05-22-2012, 10:33 AM
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Replies: 10
Views: 10,107
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...
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Forum: Bioinformatics
04-27-2012, 06:52 AM
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Replies: 10
Views: 7,113
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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