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Forum: Bioinformatics 10-26-2016, 07:12 PM
Replies: 0
Views: 945
Posted By kentnf
VirusDetect - new tool for virus discovery using deep sequencing small RNAs

We developed a new tool for virus detection using deep sequencing small RNAs. It works with both small RNA and RNA-seq data.

Compared to other tools, we extract all viruses from GenBank, and...
Forum: RNA Sequencing 05-09-2016, 06:48 AM
Replies: 1
Views: 1,592
Posted By kentnf
Find another problem for StringTie on detecting...

Find another problem for StringTie on detecting the expression of lncRNAs. One of my interesting lncRNA is a single-exon transcript, part of this lncRNA overlapped with gene region. I know this...
Forum: RNA Sequencing 05-04-2016, 11:35 AM
Replies: 1
Views: 1,592
Posted By kentnf
problem about StringTie expression

The StringTie could output expression on both gene-level (with -A parameter) and transcript-level (t_data.ctab).
The total FPKM value of gene is ~1,000,000; but the total FPKM value of transcript...
Forum: Pacific Biosciences 09-28-2015, 10:41 AM
Replies: 12
Views: 2,790
Posted By kentnf
Thanks a lot, Magdoll. You answer is very clear...

Thanks a lot, Magdoll. You answer is very clear and helpful. Now I am using the SMRTPortal version pipeline as you described. I will try the ToFU version later because it's more straightforward. BTW,...
Forum: Pacific Biosciences 09-28-2015, 07:52 AM
Replies: 12
Views: 2,790
Posted By kentnf
combine cells with same length?

Hi all,

I am new to pacbio, and recently working with iso-seq datasets. Take MFC7 as a example, I find there are 7 cells sequenced with 3-5kb. So I did analysis for each of them, then combine the...
Forum: Bioinformatics 01-09-2014, 07:53 AM
Replies: 189
Views: 71,397
Posted By kentnf
Hi tonybolger, How about add a function on...

Hi tonybolger,

How about add a function on Trimmomatic to remove the adapter of small RNA. The read is like this:

small RNA + ADAPTER

I just need the reads with adapter sequence. If the...
Forum: RNA Sequencing 07-23-2013, 10:12 AM
Replies: 7
Views: 3,437
Posted By kentnf
From the code you post. The mira does not work on...

From the code you post. The mira does not work on you server. First, check the mira program. Make sure it could be run.
Forum: Bioinformatics 04-09-2012, 08:14 AM
Replies: 2
Views: 2,009
Posted By kentnf
Hi, Wolfgang Huber I make a comparison...

Hi, Wolfgang Huber

I make a comparison between test0 and test1. All the DE genes in test1 are included in test0. I think that is the differnet variances on different estimations you metioned....
Forum: Bioinformatics 04-08-2012, 08:11 PM
Replies: 2
Views: 2,009
Posted By kentnf
Question about different results generated by DESeq.

Hi,

I have problem on DESeq, it generates different results using same dataset (without replicate), and almost same code.


Here is code for the 1st test:

conds <- factor( c(...
Forum: Bioinformatics 12-07-2011, 07:45 AM
Replies: 4
Views: 3,727
Posted By kentnf
By the way, I got another warning when analysis...

By the way, I got another warning when analysis data without replicate using DESeq.

when running below script follows the manual:
cds1<-estimateDispersions( cds1, method="blind",...
Forum: Bioinformatics 12-07-2011, 06:12 AM
Replies: 4
Views: 3,727
Posted By kentnf
How to assign values to size factor (DESeq)

I updated my DESeq recently, but got problem when assigning values (No. of total mapped read) to the size factor.

here is my code:
libsizes<-c( wt_rep1=18303917, wt_rep2=18947532,...
Forum: Bioinformatics 10-22-2011, 01:23 AM
Replies: 2
Views: 3,256
Posted By kentnf
I have the same question.

I have the same question.
Forum: 454 Pyrosequencing 09-26-2011, 09:23 PM
Replies: 3
Views: 1,990
Posted By kentnf
Thanks a lot. I checked the 454ReadStatus.txt...

Thanks a lot. I checked the 454ReadStatus.txt file. The short contigs is just like exon, one read can be mapped to two contig. That the reason why some contigs are very short, right?
Forum: 454 Pyrosequencing 09-26-2011, 11:05 AM
Replies: 3
Views: 1,990
Posted By kentnf
Very short contigs and short isotigs of newbler output.

Hi all,

I am trying to assembly ESTs using newbler 2.5. The minimum length of input ESTs is 100bp and the input ESTs have already been cleaned using seqclean. At the same time, I use the notrim...
Forum: Bioinformatics 10-29-2010, 09:35 AM
Replies: 2
Views: 1,873
Posted By kentnf
Thank you Daehwan. Before map reads to...

Thank you Daehwan.

Before map reads to genome using tophat, contamination has already been cleaned. So I use fasta as input of tophat. And then I use bowtie map forward and reverse seqs to...
Forum: Bioinformatics 10-23-2010, 08:09 PM
Replies: 2
Views: 1,873
Posted By kentnf
Different results produced by tophat?

I use tophat to map my strand-specific RNA-seq seqs and its reverse complementary seqs to genome, but the results have a little difference.

For example, I have 5700000 seqs in one sample after...
Forum: Bioinformatics 08-19-2010, 06:54 PM
Replies: 6
Views: 3,498
Posted By kentnf
the correlation of RNA-seq data.

I generated an correlation value table for all biological replicates.
Most of them have good correlation 0.9;
2-3 set around 0.8;
6-7 sets are < 0.8.

How about the data? How to improve it?...
Forum: Bioinformatics 04-27-2010, 06:25 AM
Replies: 6
Views: 4,583
Posted By kentnf
Thank you! it works. I can see the...

Thank you! it works.

I can see the different base between reference and reads, but I can't get the cell line or strain name for every reads?

I want to find the SNP between two different...
Forum: Bioinformatics 04-22-2010, 12:40 PM
Replies: 6
Views: 4,583
Posted By kentnf
I got same problem. Does anyone know how to solve...

I got same problem. Does anyone know how to solve it?
Forum: The Pipeline 10-12-2009, 11:50 AM
Replies: 5
Views: 5,478
Posted By kentnf
I also confused? 9 GBP per day = ?? mb...

I also confused?
9 GBP per day = ?? mb (million bases)
Forum: Bioinformatics 04-24-2009, 05:36 AM
Replies: 7
Views: 3,071
Posted By kentnf
up up up up up

up up up up up
Forum: Bioinformatics 04-23-2009, 10:10 AM
Replies: 7
Views: 3,071
Posted By kentnf
I use 2.9.37 version before, maybe some other...

I use 2.9.37 version before, maybe some other parameter different when I set -job:454 or sanger, now I download 2.9.44 version, use -CL:pec=yes to clip the ends of sequence, but the clipping part is...
Forum: Bioinformatics 04-22-2009, 08:02 AM
Replies: 7
Views: 3,071
Posted By kentnf
Thank you so much! sklages It work when I set...

Thank you so much! sklages
It work when I set the -job:sanger, but not work well when set -job:454.

The new problems is how to set the ends clip in MIRA,
I try -CL:emlc and -CL:emrc, some of...
Forum: Bioinformatics 04-21-2009, 10:04 AM
Replies: 7
Views: 3,071
Posted By kentnf
hehe, Thank you!

hehe, Thank you!
Forum: Bioinformatics 04-21-2009, 06:48 AM
Replies: 7
Views: 3,071
Posted By kentnf
A qusetion about denovo assembly 454 sequence using MIRA

Hi,

I use mira to do assembling on my 454 sequence, but the problem is if there are two differnet nt in the same position, the contig sequence will be change.

for example:
contig1: ...
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