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Forum: Ion Torrent 06-19-2014, 08:27 AM
Replies: 2
Views: 3,858
Posted By mbzmg1
I seem to recall seeing somewhere that the wells...

I seem to recall seeing somewhere that the wells on the P1 chip are ~1uM and the beads ~0.6uM. Someone posted some EM pictures on Seqanswers a while back but I can no longer find the post.
Forum: Ion Torrent 05-29-2014, 11:37 AM
Replies: 12
Views: 10,823
Posted By mbzmg1
Our initial attempts at using Tophat2/Bowtie2 to...

Our initial attempts at using Tophat2/Bowtie2 to map Ion Torrent RNAseq data were pretty disappointing (~30% aligned) and turned out to be biased against alignment of the longer reads (see attached...
Forum: RNA Sequencing 04-30-2014, 12:25 PM
Replies: 2
Views: 3,693
Posted By mbzmg1
Correct -the adapters that are hybridized and...

Correct -the adapters that are hybridized and ligated to your RNA fragments have degenerate overhangs that allow for strand-specific ligation, and therefore sequencing. As far as I can gather this is...
Forum: Ion Torrent 04-30-2014, 12:05 PM
Replies: 14
Views: 7,565
Posted By mbzmg1
Our polyclonal percentages are in the low to mid...

Our polyclonal percentages are in the low to mid 20s with V3 OT2 and SEQ kits.

On another note -what are people using for alignment? We have found that Bowtie2/Tophat2 do not play well with Ion...
Forum: Ion Torrent 04-16-2014, 05:33 PM
Replies: 19
Views: 7,232
Posted By mbzmg1
Have you tested it against GSNAP with Ion Torrent...

Have you tested it against GSNAP with Ion Torrent data?
I will take a look and probably test it out if mismatch etc can be set as a percentage/fraction of read length. The problem with...
Forum: Ion Torrent 04-16-2014, 04:45 PM
Replies: 19
Views: 7,232
Posted By mbzmg1
We have had success using GSNAP to map Ion...

We have had success using GSNAP to map Ion Torrent reads -especially for RNAseq with splicing. Tophat2/Bowtie2 do not deal well with Ion Torrent data.
Forum: Ion Torrent 04-16-2014, 04:35 PM
Replies: 14
Views: 7,565
Posted By mbzmg1
We have about 30 successful RNAseq runs on the...

We have about 30 successful RNAseq runs on the Ion Torrent Proton using the RNAseq v2 kit with polyA selected RNA. One modification we have made is to size select a narrower range (110-200bp) using...
Forum: Ion Torrent 04-16-2014, 04:26 PM
Replies: 2
Views: 2,413
Posted By mbzmg1
The default output format for Ion Torrent is .bam...

The default output format for Ion Torrent is .bam (even if not mapping the reads).

You need to fill out the settings for the FileExporter plugin before it will generate the .fastq files correctly....
Forum: RNA Sequencing 04-18-2013, 03:59 PM
Replies: 89
Views: 43,231
Posted By mbzmg1
I was getting the same error on Ubuntu 12.04 and...

I was getting the same error on Ubuntu 12.04 and R 2.15.3:
installation of package ‘cummeRbund’ had non-zero exit status

and can confirm that running first:
sudo apt-get install libxml2-dev...
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