Forum: Bioinformatics
10-25-2016, 03:37 AM
|
|
Replies: 16
Views: 2,706
Samtools tview
Always look at the reads, not...
Samtools tview
Always look at the reads, not just the stats. The number of unique fragments is what matters, not the duplication rate. 80% duplicates would be useless if you sequenced 2 M reads,...
|
|
Forum: SOLiD
07-05-2016, 07:55 AM
|
|
Replies: 15
Views: 10,618
The quoted error rate (<0.1%) must be after...
The quoted error rate (<0.1%) must be after reference-based correction. The problem with SOLiD was the high raw error rate of the ligation based chemistry (compared to Illumina) and the short read...
|
|
Forum: SOLiD
05-23-2016, 09:21 AM
|
|
Replies: 15
Views: 10,618
|
|
Forum: Sample Prep / Library Generation
05-19-2016, 01:28 PM
|
|
Replies: 6
Views: 1,793
|
|
Forum: Sample Prep / Library Generation
05-19-2016, 12:25 PM
|
|
Replies: 6
Views: 1,793
|
|
Forum: RNA Sequencing
04-27-2016, 03:55 AM
|
|
Replies: 15
Views: 3,806
|
|
Forum: SOLiD
04-09-2016, 05:36 AM
|
|
Replies: 13
Views: 7,337
solid reads had a high raw error rate. bowtie...
solid reads had a high raw error rate. bowtie with default settings is not ideal for 75 bp reads so 13 % seems about right. bfast will do a better job but start with trimmed reads and change...
|
|
Forum: Bioinformatics
04-06-2016, 12:07 AM
|
|
Replies: 20
Views: 11,964
I don't remember exactly how many mismatches...
I don't remember exactly how many mismatches bowtie1 tolerates, it should work but you may have to change some settings if you have lots of mismatches at the end, hence my suggestion to try mapping...
|
|
Forum: Bioinformatics
04-05-2016, 10:01 AM
|
|
Replies: 20
Views: 11,964
|
|
Forum: Epigenetics
12-28-2015, 03:56 AM
|
|
Replies: 6
Views: 3,564
|
|
Forum: SOLiD
12-19-2015, 02:33 AM
|
|
Replies: 1
Views: 6,675
|
|
Forum: Oxford Nanopore
10-28-2015, 08:00 AM
|
|
Replies: 13
Views: 5,456
|
|
Forum: Pacific Biosciences
10-07-2015, 10:18 AM
|
|
Replies: 62
Views: 29,346
|
|
Forum: Epigenetics
09-05-2015, 03:53 PM
|
|
Replies: 2
Views: 1,992
Yes, it is common. Just look at some ENCODE...
Yes, it is common. Just look at some ENCODE datasets. Sort of like FAIRE. You should expect your ChIP peaks to be much higher though. Would guess PAF1 has a few good sites at ~- 500 bp that averages...
|
|
Forum: Bioinformatics
06-20-2015, 02:45 PM
|
|
Replies: 14
Views: 7,983
|
|
Forum: De novo discovery
06-08-2015, 12:36 PM
|
|
Replies: 5
Views: 7,994
|
|
Forum: Sample Prep / Library Generation
06-03-2015, 02:16 PM
|
|
Replies: 1
Views: 969
Why not use dynabeads directly? They...
Why not use dynabeads directly? They (Invitrogen/Ambion/Life/thermo or whatever they are called now) have a mRNA direct kit that is much cheaper than buying beads only.
|
|
Forum: Sample Prep / Library Generation
05-26-2015, 10:38 PM
|
|
Replies: 4
Views: 1,367
|
|
Forum: Bioinformatics
05-07-2015, 02:41 PM
|
|
Replies: 16
Views: 7,074
|
|
Forum: Bioinformatics
04-27-2015, 03:04 AM
|
|
Replies: 16
Views: 7,074
|
|
Forum: Bioinformatics
04-24-2015, 12:20 PM
|
|
Replies: 16
Views: 7,074
Reading the manual is also a good start:
-m...
Reading the manual is also a good start:
-m <int>
Suppress all alignments for a particular read or pair if more than <int> reportable alignments exist for it. Reportable alignments are those that...
|
|
Forum: Bioinformatics
04-24-2015, 07:41 AM
|
|
Replies: 16
Views: 7,074
|
|
Forum: Bioinformatics
04-24-2015, 07:22 AM
|
|
Replies: 16
Views: 7,074
|
|
Forum: Ion Torrent
04-21-2015, 09:25 AM
|
|
Replies: 122
Views: 112,765
|
|
Forum: Sample Prep / Library Generation
04-17-2015, 10:37 AM
|
|
Replies: 3
Views: 1,434
I have sequenced some libraries that were > 1 y...
I have sequenced some libraries that were > 1 y old without problem but of course it is no guarantee. But in this case it does not make sense to me to take one replicate to 15 M reads instead of 3x5M.
|
