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Search: Posts Made By: SOLiDance
Forum: General 03-30-2017, 08:36 PM
Replies: 4
Views: 1,514
Posted By SOLiDance
1. Have you tried with the reverse-complement...

1. Have you tried with the reverse-complement sequence of your target?
2. It should be related with threshold setting of the UAS software suite on FGx, I highly recommend you to read its user guide...
Forum: Pacific Biosciences 09-21-2015, 11:38 PM
Replies: 3
Views: 1,427
Posted By SOLiDance
Thumbs up Thanks a lot!

Thanks a lot!
Forum: Pacific Biosciences 09-19-2015, 06:31 PM
Replies: 3
Views: 1,427
Posted By SOLiDance
How does SMRT cell detect fluorescent signal?

Hi I have a question about the signal detection in ZMW.
It's said that "The ZMW holes are ~70 nm in diameter and ~100 nm in depth...the wavelength of the light is too large to allow it efficiently...
Forum: General 07-18-2013, 09:46 PM
Replies: 1
Views: 843
Posted By SOLiDance
For NGS, the reads are normally short. For...

For NGS, the reads are normally short. For assembly, many reads will be rearranged and constructed into contigs. So, it not like we "need" contigs. Actually, the contigs are just results of assembly....
Forum: General 07-24-2012, 02:04 AM
Replies: 6
Views: 3,228
Posted By SOLiDance
Really? It's pretty serious one, Thanks! I'll...

Really? It's pretty serious one, Thanks! I'll keep it in mind
Forum: Bioinformatics 03-13-2012, 05:10 PM
Replies: 8
Views: 3,246
Posted By SOLiDance
Smile Thank u~ yeah,I though blast+ won't need much...

Thank u~ yeah,I though blast+ won't need much compute resource,so ran on A 4-threads i5 cpu+8G RAM. Fortunately,I do have account to a cluster. :) Thanks for your help ~
Forum: Bioinformatics 03-13-2012, 04:53 PM
Replies: 8
Views: 3,246
Posted By SOLiDance
No,don't have annotated genome.But we believed...

No,don't have annotated genome.But we believed it's genome was quite similar with Takifugu rubripes(puffer).
And,these transcripts are differentially expressed ones which I found after diff_exp...
Forum: Bioinformatics 03-13-2012, 05:40 AM
Replies: 8
Views: 3,246
Posted By SOLiDance
some kind of fish,similar to pufferfish(fugu)

some kind of fish,similar to pufferfish(fugu)
Forum: Bioinformatics 03-13-2012, 05:15 AM
Replies: 8
Views: 3,246
Posted By SOLiDance
Are you sure about this? I'm sorry,but I just...

Are you sure about this?
I'm sorry,but I just took a look at this website. The first step of Gorilla is to choose organism from 8 provided ones, of course mine is not there yet~
and also it's...
Forum: Bioinformatics 03-13-2012, 04:32 AM
Replies: 8
Views: 3,246
Posted By SOLiDance
Smile Recommend soft for GO enrichment & results visualization

Hi~everyone
I'm doing some transcriptome work,already have a bunch of transcript ID and corresponding GO IDs.
Now I need statistical information for GO categories and want to visualized some...
Forum: Bioinformatics 01-11-2012, 04:14 PM
Replies: 13
Views: 8,058
Posted By SOLiDance
emm~ Me too,bioscope can always get obvious...

emm~ Me too,bioscope can always get obvious higher map rate, I doubt maybe it contains more false positive mapped reads :D
Forum: Bioinformatics 01-10-2012, 04:43 PM
Replies: 0
Views: 1,437
Posted By SOLiDance
anybody know this 5th Virtual Training Workshop on Bioinfo?

Hi,there~
I got some e-mail about 5th virtual training workshop on bioinformatics ,here is the link (http://www.abren.net/workshop/). Maybe someone needed it.
I already registered an account....
Forum: Bioinformatics 01-05-2012, 05:06 PM
Replies: 13
Views: 8,058
Posted By SOLiDance
Thanks for the info. I indeed Not noticed there's...

Thanks for the info. I indeed Not noticed there's a NEWS file~ shoot,My fault!
Forum: Bioinformatics 01-05-2012, 04:53 PM
Replies: 13
Views: 8,058
Posted By SOLiDance
Thanks for yr help! Actually, I used the -c ,even...

Thanks for yr help! Actually, I used the -c ,even tried -n 3 or -n4 when proceed bwa aln.Sorry for forget to mention it~
I checked my bwa version, it's 0.6.1, maybe here is the reason,what a...
Forum: Bioinformatics 01-04-2012, 11:14 PM
Replies: 13
Views: 8,058
Posted By SOLiDance
bwa:how to align color space reads

Hi,everybody~
This puzzled me for days : I tried to use bwa on SOLiD seq results. But when I finished the manual, couldn't find a in-detail workflow about color space reads alignment. According...
Forum: Pacific Biosciences 11-22-2011, 04:00 PM
Replies: 5
Views: 3,320
Posted By SOLiDance
Thanks for the link! But I still worry about...

Thanks for the link!
But I still worry about how helpful it can be with such a high error rate~
Maybe 454 is better choice since the read length can be more than 500bp and hybrid assemble pipeline...
Forum: Pacific Biosciences 11-21-2011, 05:18 PM
Replies: 5
Views: 3,320
Posted By SOLiDance
Thank for GenoMax , our lab is planning to do a...

Thank for GenoMax , our lab is planning to do a denovo sequencing, Prof. wanna add some Pacbio data , but now I'm afraid it won't help us much~
Forum: Bioinformatics 11-20-2011, 11:22 PM
Replies: 0
Views: 963
Posted By SOLiDance
Need help for GO term~

Hi,everyone~
I got some transcriptome data to analyse.
Now need to do GO & kegg.But on the GO website I can't find annotation database for my specie.
Does anyone how to do GO term like this? Do...
Forum: SOLiD 11-20-2011, 04:50 PM
Replies: 3
Views: 2,377
Posted By SOLiDance
1) Can't use custom barcodes;cause you can only...

1) Can't use custom barcodes;cause you can only select barcode Num,but not input barcode sequence when you set up a seq run on the SOLiD machine~
2) agreed with phillip
Forum: Pacific Biosciences 11-20-2011, 04:13 PM
Replies: 5
Views: 3,320
Posted By SOLiDance
Parameters of PaciBio

Hi,everyone! Does anyone know anything about the Pacific Bio seq instrument work stats? I knew the error rate is about 15% one year ago.
I wonder has it been improved now? If i wanna control the...
Forum: Bioinformatics 07-14-2011, 04:41 AM
Replies: 4
Views: 2,774
Posted By SOLiDance
Maybe you should try re-index the bam file with...

Maybe you should try re-index the bam file with the same ref? For example: samtools faidx ref.fasta, then use the .fai to get the sorted bam?
I'm just a beginner,not sure about it~ Hope can help
Forum: Bioinformatics 05-12-2011, 10:49 PM
Replies: 4
Views: 2,304
Posted By SOLiDance
Thanks for your info~ yesterday I encountered...

Thanks for your info~
yesterday I encountered with new trouble. Later, we found it's VERY important to make sure that *.fa files have same order in CMAP and BAM. After fixed the script to get new...
Forum: SOLiD 05-11-2011, 06:36 PM
Replies: 0
Views: 1,437
Posted By SOLiDance
Sth about RNA Barcode library

:) Hello everyone~
I am gonna prep several RNA Barcode libraries(fragment), The protocol is simple and almost the same as the normal RNA libraries(fragment).
It's said the IA sequence will anneal...
Forum: SOLiD 05-11-2011, 06:00 PM
Replies: 7
Views: 2,724
Posted By SOLiDance
Fabian is rt, Bioscope is quite easy to...

Fabian is rt, Bioscope is quite easy to learn&use. It's free with the SOLiD instrument,and only can be installed on computer clusters,not a laptop or desktop(Just heared, didn't try it~)
Forum: Ion Torrent 05-11-2011, 05:56 PM
Replies: 2
Views: 5,155
Posted By SOLiDance
GOOD JOB! I heared 318 chip will be released...

GOOD JOB! I heared 318 chip will be released soon~ Hav longer reads and higher quality~
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