Forum: Bioinformatics
05-08-2019, 07:02 AM
|
|
Replies: 2
Views: 1,733
Colin, thanks a lot for your input! ...
Colin, thanks a lot for your input!
(Unfortunately for now I had to switch to STAR because it's hard to get help for BBmap questions while STAR's author is very responsive and helpful)
|
|
Forum: Bioinformatics
04-01-2019, 01:04 AM
|
|
Replies: 2
Views: 1,733
Wrong mapping with BBmap default parameters
I performed mapping for my RNA-seq data (150 bp reads) with BBMap, just the default parameters (the only special parameter set was low memory):
bbmap.sh ref=gencode.v29.transcripts.fa...
|
|
Forum: Bioinformatics
03-29-2019, 07:44 AM
|
|
Replies: 679
Views: 215,277
I'm wondering if anyone tried to apply...
I'm wondering if anyone tried to apply callvariants.sh to RNA-seq data. When I tried to use it with my bam file, it found about 140,000 variants - but all of them are homozygous which is obviously...
|
|
Forum: Bioinformatics
02-25-2019, 06:32 PM
|
|
Replies: 335
Views: 158,401
sorry for another dummy question, but I really...
sorry for another dummy question, but I really want to understand how bbduk works and currently I'm having troubles with that... Below I list example of 11 reads containing adapter sequence which I...
|
|
Forum: Bioinformatics
02-25-2019, 05:14 PM
|
|
Replies: 335
Views: 158,401
|
|
Forum: Bioinformatics
02-25-2019, 02:30 PM
|
|
Replies: 335
Views: 158,401
Thank you @GenoMax!
What would be the main...
Thank you @GenoMax!
What would be the main advantage of using bbsplit instead of bbduk? As I understand, BBSplit internally uses BBMap, unlike BBDuk - but what would it practically mean? In my...
|
|
Forum: Bioinformatics
02-25-2019, 12:01 PM
|
|
Replies: 335
Views: 158,401
Hello,
I was trying to filter out rRNA reads...
Hello,
I was trying to filter out rRNA reads using the command like this:
where ribokmers.fa.gz is taken from Brian's googledrive link posted at https://www.biostars.org/p/159959/
I noticed...
|
|
Forum: Sample Prep / Library Generation
05-12-2011, 04:50 AM
|
|
Replies: 6
Views: 4,205
quoting the wiki...
quoting the wiki (http://en.wikipedia.org/wiki/Auto-defrost#Disadvantages), "In laboratories, self-defrosting freezers must not be used to store certain delicate reagents such as enzymes, because the...
|
|
Forum: Sample Prep / Library Generation
05-10-2011, 02:05 AM
|
|
Replies: 8
Views: 5,371
I will be very thankful to hear any news about...
I will be very thankful to hear any news about your experience on deep sequencing of plasma miRNA as I will probably try to do the same (also on SOLiD) in future.
Good luck and all the best for...
|
|
Forum: Sample Prep / Library Generation
05-08-2011, 10:18 AM
|
|
Replies: 8
Views: 5,371
|
|
Forum: SOLiD
05-06-2011, 04:56 AM
|
|
Replies: 36
Views: 45,035
|
|
Forum: SOLiD
05-05-2011, 09:02 PM
|
|
Replies: 36
Views: 45,035
|
|
Forum: SOLiD
05-05-2011, 03:28 PM
|
|
Replies: 36
Views: 45,035
|
|
Forum: SOLiD
05-05-2011, 03:06 PM
|
|
Replies: 36
Views: 45,035
ok, finally I found by myself :)
according to...
ok, finally I found by myself :)
according to published patent 20100279305, adaptor oligo mix contains
1) 5'-CCUCUCUAUGGGCAGUCGGUGAU (3.1 μM)
2) 5'-NNNNNNATCACCGACTGCCCATAGAGAGG (6.1 μM)
3)...
|
|
Forum: SOLiD
05-05-2011, 11:43 AM
|
|
Replies: 36
Views: 45,035
|
|
Forum: SOLiD
05-05-2011, 08:57 AM
|
|
Replies: 36
Views: 45,035
|
|
Forum: Ion Torrent
05-05-2011, 05:49 AM
|
|
Replies: 25
Views: 24,651
|
|
Forum: Ion Torrent
05-05-2011, 05:03 AM
|
|
Replies: 25
Views: 24,651
|
|
Forum: The Pipeline
11-25-2010, 10:42 AM
|
|
Replies: 4
Views: 7,016
|
|
Forum: The Pipeline
11-24-2010, 11:47 AM
|
|
Replies: 4
Views: 7,016
|
|
Forum: The Pipeline
11-19-2010, 09:18 AM
|
|
Replies: 4
Views: 7,016
Can Ion Torrent be useful for microRNA sequencing?
Dear colleagues,
what do you think about applicability of Ion Torrent for miRNA profiling? They promise "Thousands to Millions of moderate reads per sample". "Moderate reads" is even excessive here,...
|
