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Forum: Bioinformatics 05-13-2014, 06:54 AM
Replies: 18
Views: 13,489
Posted By sidderb
As Simon reads these I just wanted to flag up...

As Simon reads these I just wanted to flag up that I have run into the same issue with a position sorted alignment from STAR as well.

I was so excited to see this feature in 0.6 as the position...
Forum: Bioinformatics 07-31-2013, 01:50 AM
Replies: 2
Views: 1,737
Posted By sidderb
Just to close this off - turned out to be an...

Just to close this off - turned out to be an issue with the CRO's sequencer and they are having to re-sequence our samples. Bit worrying that they didn't pick this up themselves...
Forum: Bioinformatics 07-30-2013, 12:44 AM
Replies: 2
Views: 1,737
Posted By sidderb
RRBS missing enz site

We've just had some RRBS data returned for the first time. I am told by the CRO that it's a non-directional, Msp1 library. My head is swimming from trying to work out the combinations of read pairs...
Forum: Bioinformatics 04-11-2013, 08:59 AM
Replies: 5
Views: 3,071
Posted By sidderb
Have you tried Picard's...

Have you tried Picard's CollectAlignmentSummaryMetrics & CollectRnaSeqMetrics?

http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentSummaryMetrics
Forum: Bioinformatics 04-04-2013, 02:43 AM
Replies: 1
Views: 1,494
Posted By sidderb
iGenomes update cycle?

Does anyone know if and when the Illumina iGenomes annotation sets (http://tophat.cbcb.umd.edu/igenomes.html) will be updated? I'm specifically interested in the rat genome which has a new build...
Forum: Sample Prep / Library Generation 04-26-2012, 03:54 AM
Replies: 28
Views: 21,684
Posted By sidderb
Does anyone worry about the quantification of...

Does anyone worry about the quantification of expression from total RNA versus ploy A enriched RNA?

I imagine that you would inflate your expression values from total RNA by including reads from...
Forum: Bioinformatics 04-11-2012, 07:07 AM
Replies: 3
Views: 3,606
Posted By sidderb
i have found the illumina bodymap2 data to be a...

i have found the illumina bodymap2 data to be a good test set. This includes multiple formats (SE/PE) from 16 human tissues.
...
Forum: Bioinformatics 04-11-2012, 02:12 AM
Replies: 0
Views: 2,204
Posted By sidderb
cross species RNAseq

Hi All,

I have paired-end RNAseq data from the same tissue in two species (human and rat), which I want to compare. It seems to me this is fraught with issues:


The annotation quality for...
Forum: Bioinformatics 04-10-2012, 04:18 AM
Replies: 9
Views: 4,740
Posted By sidderb
~60% in all samples

~60% in all samples
Forum: Bioinformatics 04-09-2012, 12:30 PM
Replies: 9
Views: 4,740
Posted By sidderb
Can anyone help?

Can anyone help?
Forum: Bioinformatics 04-05-2012, 02:40 AM
Replies: 9
Views: 4,740
Posted By sidderb
Interpreting 5'/3' bias

Hi All,
We have 100bp PE RNAseq data generated on a HiSeq2000 from a library prepped with the Nugen Ovation v2 kit. The samples are from human and rat, with the human samples of lesser quality...
Forum: Bioinformatics 03-22-2012, 08:49 AM
Replies: 6
Views: 3,911
Posted By sidderb
It took me a week to drill back through my...

It took me a week to drill back through my pipeline and work out these files were messing it up. In the end I got a fresh genome and GTF from ensembl, then used custom scripts to build all the...
Forum: Bioinformatics 03-20-2012, 10:03 AM
Replies: 6
Views: 8,396
Posted By sidderb
how to create interval lists for picard?

Hi,

I need a rRNA interval list file for picard's CollectRnaSeqMetrics, as defined here (http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html). Is there a handy tool to...
Forum: Bioinformatics 08-03-2011, 08:05 AM
Replies: 0
Views: 1,066
Posted By sidderb
software for chip-pcr analysis

Hi All,

I realise this might be a bit low tech for this forum, but has anyone come across a good R package for the analysis of chip-pcr arrays?

Many thanks
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