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Forum: Bioinformatics 11-20-2018, 11:52 PM
Replies: 0
Views: 223
Posted By huan
Smile How to convert my ratio vector(ratio1,ratio2,ratio3,...) to binary vector?

Hi all,
I have a joint CpG sites methylation ratio vector (ratio1,ratio2,ratio3,...) from WGBS data. Now I want to use a binary value 1 or 0 represents methylated and unmethylaoted status and ...
Forum: Pacific Biosciences 11-28-2017, 06:37 PM
Replies: 4
Views: 2,002
Posted By huan
I really appreciate for your help! I will have a...

I really appreciate for your help! I will have a try!
Forum: Pacific Biosciences 11-22-2017, 02:05 AM
Replies: 4
Views: 2,002
Posted By huan
Is it possible to evaluate genome size with sequel data?

Now we are doing the denovo assembly of marine organism with whole genome sequcing using sequel system. As we all know, the DNA extraction from marine organism is very difficult because of pollution...
Forum: De novo discovery 11-22-2017, 01:45 AM
Replies: 0
Views: 1,656
Posted By huan
Is it possible to evaluate genome size Using degradated DNA?

Hi,
To evaluate the size and heterozygus rate of an Mollusca sample, we are going to do the NGS sequence with illumina Hiseq plateform. It is known that the DNA extraction from Mollusca sample...
Forum: Pacific Biosciences 03-08-2017, 11:45 PM
Replies: 0
Views: 961
Posted By huan
Question How can I group my transcript from gffcompare result?

Hello,
I am new to gffcompare/cuffcompare and now I am confused with the output file.
I have used SMRTAnalysis Iso-Seq pipline to get isoforms from pacbio sequencing data. Now I want to classify...
Forum: Bioinformatics 09-19-2016, 08:05 PM
Replies: 0
Views: 724
Posted By huan
Quantification for transcirpt without reference genome.

Hello, every one!
I have got the transcript downloaded form NCBI. Also we have got the RNA-Seq data from illumina platform. Now we want quantify the transcript with short reads. Since we don't have...
Forum: Pacific Biosciences 09-19-2016, 07:47 PM
Replies: 0
Views: 1,212
Posted By huan
how can I get abundance from both Iso-seq output and illumina data?

Hi,
We've got the done the RNA-seq of a species (genome is about 3GB), but NO reference genome is available, using pacbio and Illumina. After the RS_IsoSeq and cd-hit analysis, we have redundant...
Forum: Pacific Biosciences 06-27-2016, 12:19 AM
Replies: 1
Views: 1,345
Posted By huan
Why the pacbio isoseq data used for RNA analysis is much more than illumina data?

As we all know, for the human RNA-seq analysis, 4-6G clean data from illumina platform is enough. But when I use pacbio's ISO-seq pipline, the subread data is more than 10 times the amount of...
Forum: Pacific Biosciences 06-22-2016, 08:10 PM
Replies: 2
Views: 2,053
Posted By huan
Now we have a lab the loading p1 has been above...

Now we have a lab the loading p1 has been above 70%:
Prod=0 ZMWs: 9.675%
Prod=1 ZMWs: 76.32%
Prod=2 ZMWs: 14.01%
Total Active ZMWs: 90.32%
I can not figure out it is good or not. Is there any...
Forum: Pacific Biosciences 06-02-2016, 03:56 AM
Replies: 1
Views: 1,119
Posted By huan
Does the Mixed samples effects the IsoSeq Analysis?

Hi, pacbio
Recently we got the mixed wheat samples with different treatment and used the SMRT(Pacific Biosciences) sequencing system PacBio RS II to generate cDNA sequences for the mixed sample. We...
Forum: Pacific Biosciences 04-16-2016, 07:22 PM
Replies: 2
Views: 2,053
Posted By huan
How much of PacBio ZMW Loading Productivity 1(p1) is best for IsoSeq?

Hi,
Now I am investigateing the IsoSeq in PacBio platform. I find that the ZMW Loading Productivity 1(P1) varies a lot from different experiments. So I am confused what's the normal range for P1....
Forum: Bioinformatics 04-07-2016, 12:35 AM
Replies: 0
Views: 728
Posted By huan
The difference between gene loci with isoform in RNA-seq alternative anlalysis?

As I know, 'A locus (plural loci), in genetics, is the specific location or position of a gene, DNA sequence, on a chromosome. Gene loci analysis is generally done in DNA seq. But recently, I have...
Forum: Bioinformatics 04-06-2016, 11:15 PM
Replies: 0
Views: 551
Posted By huan
GMAP result with multi-mapping?

I have used GMAP to mapping my RNA-seq data to the reference genome with parameter ( -f samse -z sense_force -t 5 -n 0 --cross-species --allow-close-indels 0 ) to get SMA output ,but I have many...
Forum: Bioinformatics 02-22-2016, 12:54 AM
Replies: 0
Views: 607
Posted By huan
Tools to predict genes with RNA sequence

I have got a set of transcript sequence from RNA-seq in fasta. The referenced genome sequence is also known. Now I want to discover new genes from the transcript sequence. So Is there any tools...
Forum: Bioinformatics 01-20-2016, 10:34 PM
Replies: 21
Views: 5,637
Posted By huan
@chris_s I have met the same error and have...

@chris_s I have met the same error and have solved by your sollution. Thanks a lot!
BTW, have you found the reason why this error occours in the formatdb? Thanks a lot.
Forum: Pacific Biosciences 01-19-2016, 04:57 PM
Replies: 1
Views: 2,087
Posted By huan
How can I calcualte the sequence identity and coverage form GMAP output bam file?

Now I have got a bam file from gmap alignment with data from pacbio isoseq result. Now I want to get the statistic information about the coverage and identity of every sequence. So is there any...
Forum: Illumina/Solexa 12-29-2015, 05:34 PM
Replies: 2
Views: 1,544
Posted By huan
Thanks a lot @Brian Bushnell. You did inspire me....

Thanks a lot @Brian Bushnell. You did inspire me. I'll have a try.
Thanks again.
Forum: Illumina/Solexa 12-28-2015, 05:58 PM
Replies: 2
Views: 1,544
Posted By huan
illumina aligment ratio reduced when increase insert size

We build two different cDNA library for the same sample with different size(196 and 225) for pair end sequencing by Hiseq with the same sequence length 126. Then we map the two set of sequencing data...
Forum: RNA Sequencing 12-28-2015, 04:01 AM
Replies: 0
Views: 1,344
Posted By huan
tophat2 aligment ratio reduced when increase insert size

Now I have two set of HiSeq pair end equencing data for the same sample with different insert size(196 and 225). The I use tophat2 to align the reads to the genome seperately, the tophat2 parameter...
Forum: RNA Sequencing 12-27-2015, 11:00 PM
Replies: 8
Views: 3,766
Posted By huan
Thanks a lot kmcarr. Your answer really works...

Thanks a lot kmcarr. Your answer really works great.
Forum: RNA Sequencing 12-23-2015, 05:59 PM
Replies: 8
Views: 3,766
Posted By huan
I got it. Thanks kmcarr. But I wonder I will...

I got it. Thanks kmcarr.
But I wonder I will lose a lot low expressed transcript if I filter after the Trinity assembly is complete. Does it influence my analysis? BTW, if I filter before assemble,...
Forum: Pacific Biosciences 12-22-2015, 11:28 PM
Replies: 5
Views: 2,328
Posted By huan
Thanks a lot for your reply@bowhan...

Thanks a lot for your reply@bowhan @nucacidhunter.
That's quite a great idea to ensure the integrity of 5' end by library building.
But what I want is to deal with it by analysis...
Forum: RNA Sequencing 12-22-2015, 11:16 PM
Replies: 8
Views: 3,766
Posted By huan
Thanks a lot @kmcarr. That's quite a good idea....

Thanks a lot @kmcarr.
That's quite a good idea. But I am not sure whether the "removing contigs" means 'removing inchworm result contigs with --no_run_butterfly --no_run_quantifygraph' or not....
Forum: Pacific Biosciences 12-22-2015, 01:46 AM
Replies: 5
Views: 2,328
Posted By huan
Thanks a lot @bowhan Yes. I have do the size...

Thanks a lot @bowhan
Yes. I have do the size selection. But we still can't fully sequence the entire lengths of long transcript. Trunction of sequence could occur form RNA defradation,mechanical...
Forum: RNA Sequencing 12-21-2015, 06:04 PM
Replies: 8
Views: 3,766
Posted By huan
Thanks a lot @arthurmelo. We have filted the ...

Thanks a lot @arthurmelo.
We have filted the low quality reads by deleting the percentage of Phred score Q>20 less than 80%. So As you suggest, we'd better fillter the reads again by Trimmomatic....
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