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Forum: Illumina/Solexa 02-08-2013, 12:50 PM
Replies: 1
Views: 1,252
Posted By byou678
Do we need two DIFFERENT adapters to generate Pair-end Reads ?

Hi All,

I am wondering: Must we have at least two Different adapters to generate Pair-end Reads(Take Illumina Platform for example) ?


I found this tread in SEQanswers below...
Forum: Bioinformatics 02-07-2013, 07:03 AM
Replies: 4
Views: 1,660
Posted By byou678
Thumbs up Thanks for the reply!! Futhur, must we have...

Thanks for the reply!!

Futhur, must we have at least two DIFFERENT adapters to generate Pair-end Reads(Take Illumina Platform for example) ?
Forum: Bioinformatics 02-06-2013, 02:57 PM
Replies: 4
Views: 1,660
Posted By byou678
Arrow Do we need two DIFFERENT adapters to generate Pair-end Reads ?

Hi All,

I am wondering: Must we have at least two adapters to generate Pair-end Reads(Take Illumina Platform for example) ?
I am also not sure about using other Platforms.

I found this tread...
Forum: Bioinformatics 01-29-2013, 01:45 PM
Replies: 1
Views: 1,159
Posted By byou678
Any help??

Any help??
Forum: Bioinformatics 01-28-2013, 01:16 PM
Replies: 1
Views: 1,159
Posted By byou678
Arrow Need run DESeq in Galaxy? Please Help!

Hi All,

Could anyone tell Which Version Galaxy has the function to run DESeq (determine differentially expressed transcripts from read alignments)?:confused:

As far as I know, Penn State...
Forum: Bioinformatics 01-28-2013, 12:57 PM
Replies: 17
Views: 4,796
Posted By byou678
Could anyone tell Which Version Galaxy has the...

Could anyone tell Which Version Galaxy has the function to run DESeq?

As far as I know, Penn State Version doesn't integrate the DESeq function, and Ratsch Lab Version does not work recently.
...
Forum: Bioinformatics 11-01-2012, 12:17 PM
Replies: 6
Views: 2,004
Posted By byou678
Could anyone give the general coverage...

Could anyone give the general coverage requirement criteria for alignment?

Thanks.
Forum: Bioinformatics 10-30-2012, 08:02 AM
Replies: 1
Views: 1,477
Posted By byou678
Question How to check HCV genomic sequences between Two samples is different or not?

I am looking to determine if the Hepatitis C Virus genomic sequences (variant population structure) between two samples is different to a statistically significant degree.

If the nucleotide...
Forum: Bioinformatics 10-23-2012, 12:02 PM
Replies: 5
Views: 15,628
Posted By byou678
Arrow Thanks for your reply. But i think we can...

Thanks for your reply.
But i think we can convert FASTQ to FASTA, Any other response to confirm it?

Take a look at this link ( FASTQ to FASTA ):...
Forum: Bioinformatics 10-19-2012, 01:45 PM
Replies: 5
Views: 15,628
Posted By byou678
Thumbs up Thanks a lot for your reply! After adding >...

Thanks a lot for your reply!

After adding > on the first line in the TXT file, How can u save it to FASTA file (with .fasta extension)?

In addition, if there are Thousands of reads/sequences in...
Forum: Bioinformatics 10-19-2012, 01:32 PM
Replies: 5
Views: 15,628
Posted By byou678
Arrow Need Sequence Format Converter

Hi All,

Could anyone recommend the Online Sequence Format Converter?

For example, I would like to convert sequence TXT file to FASTA file, or FASTA to FASTQ. After conversion, I need download...
Forum: Ion Torrent 10-15-2012, 07:54 AM
Replies: 5
Views: 10,247
Posted By byou678
Thanks very much for your info, arolfe.

Thanks very much for your info, arolfe.
Forum: Ion Torrent 10-12-2012, 06:04 AM
Replies: 5
Views: 10,247
Posted By byou678
Done. Thanks. Could anyone give me some...

Done. Thanks.

Could anyone give me some ideas? I really appreciate it!
Forum: Ion Torrent 10-11-2012, 01:07 PM
Replies: 5
Views: 10,247
Posted By byou678
Arrow Ion Torrent PGM Analysis Pipeline

Hi Everyone,

If anyone has Ion Torrent PGM data analysis experience here, could you please share your general/standard Analysis Pipeline? Thanks for any response!!

In addition, what kind of...
Forum: Ion Torrent 08-07-2012, 07:40 AM
Replies: 2
Views: 6,451
Posted By byou678
https://learn.appliedbiosystems.com/semiconductors...

https://learn.appliedbiosystems.com/semiconductorsequencing
You can find Web-Based Training in the link above. Best wishes.
Forum: Ion Torrent 07-27-2012, 11:52 AM
Replies: 27
Views: 18,792
Posted By byou678
Thumbs up Thanks for your info and advice.

Thanks for your info and advice.
Forum: Literature Watch 10-14-2011, 07:33 AM
Replies: 6
Views: 5,085
Posted By byou678
I am in the same boat. It takes a very long time...

I am in the same boat. It takes a very long time for relatively large data/file. But using only the first 60 genes of the example/demo data, i get the result after about 3 mins (choose only one...
Forum: Bioinformatics 10-11-2011, 07:13 AM
Replies: 0
Views: 1,946
Posted By byou678
Question How to combine two Reference Genome (Files)?

Hi everyone,

I have two reference (genome) files. Let's say EAB_FB_MG.fa(total37972 sequences/contigs) and EAB_FB.fa(21272 sequences/contigs). I know there are some common contigs between them....
Forum: Bioinformatics 10-07-2011, 08:08 AM
Replies: 17
Views: 4,796
Posted By byou678
Wink I installed DESeq (1.4.1) after running the codes...

I installed DESeq (1.4.1) after running the codes below in R2.13.2.( to update all installed packages that are out of date)

source("http://bioconductor.org/biocLite.R")...
Forum: Bioinformatics 10-07-2011, 07:41 AM
Replies: 17
Views: 4,796
Posted By byou678
Smile I had the similar problems as you and figured it...

I had the similar problems as you and figured it out by using the old version manual (2010-01-19) with R2.11.1. Forget the "normalized" and " estimateDispersions" now:) Maybe somebody can use both...
Forum: Bioinformatics 10-04-2011, 07:42 PM
Replies: 4
Views: 2,022
Posted By byou678
Thumbs up Thanks again ECO. Yes, I like using R too and I...

Thanks again ECO. Yes, I like using R too and I have figured it out.
Forum: Bioinformatics 10-03-2011, 11:57 AM
Replies: 4
Views: 2,022
Posted By byou678
Arrow Thanks ECO, I run the similar codes in R, too....

Thanks ECO, I run the similar codes in R, too. And I can get the result like yours Just based on the Spreadsheets showed in this thread. Sorry for not telling more info about my data:But I have more...
Forum: Bioinformatics 10-03-2011, 07:53 AM
Replies: 4
Views: 2,022
Posted By byou678
Question How to extract Common Genes from 2 spreadsheets

Now I have two Excel spreadsheets, parts of them are as below:

Spreadsheet1

Gene Change Padj
1 212 0.0006
2 99 0.09
3 15 0.7
4 59 ...
Forum: RNA Sequencing 09-29-2011, 12:26 PM
Replies: 13
Views: 15,068
Posted By byou678
Talking Kerhard's post make sense! I also read "Analysing...

Kerhard's post make sense! I also read "Analysing RNA-Seq data with the 'DESeq' package". And I have another question: All the Codes using DESeq
in R is for the Example with Replicates. like
Then,...
Forum: Bioinformatics 09-27-2011, 08:03 AM
Replies: 2
Views: 2,726
Posted By byou678
Arrow Thanks for your help, tnabtaf! However I...

Thanks for your help, tnabtaf!

However I don't have the Annotation file. And I think I can generate pileup file from BAM dataset, then use PILEUP COUNTS ( Pileup Compare counting reads mapped per...
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