SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 14 of 14
Search took 0.00 seconds.
Search: Posts Made By: asling
Forum: Core Facilities 12-16-2011, 05:38 AM
Replies: 7
Views: 4,076
Posted By asling
Thanks for your reminding. It is really a problem...

Thanks for your reminding. It is really a problem if too many primer ended DNA is prefered by library preparation, especially the final product DNA size by using this kit varies from 200bp to 1500bp,...
Forum: Core Facilities 12-14-2011, 11:06 PM
Replies: 7
Views: 4,076
Posted By asling
In the manul of Sigma, they only say after the...

In the manul of Sigma, they only say after the fragmentation of chromosome DNA, OmniPlex Library is then PCR amplified using universal oligonucleotide primers and a limited number of cycles, it seems...
Forum: Bioinformatics 12-14-2011, 07:30 AM
Replies: 0
Views: 2,581
Posted By asling
sequencing a single chromosome

Hi!

We plan to sequence a single chromosome of a mammal. Our purpose is not to profile the whole chromosome, but to get a specific region's sequence in the separated chromosome.

Here is our...
Forum: Core Facilities 12-14-2011, 07:22 AM
Replies: 7
Views: 4,076
Posted By asling
hi! We also plan to sequence a single...

hi!
We also plan to sequence a single chromosome by using Sigma GenomePlex Single Cell Whole Amplification Kit. However our purpose is not to profile the whole chromosome, but to get a specific...
Forum: Bioinformatics 12-11-2011, 11:21 PM
Replies: 6
Views: 3,916
Posted By asling
Any suggestion?

Any suggestion?
Forum: Bioinformatics 12-09-2011, 03:54 AM
Replies: 6
Views: 3,916
Posted By asling
fetch transcripts assembled by cufflinks

Hi!

I am an user of cufflinks. It's quite a good tool to estimate gene differential expression. However, our purpose is not only to test differentially expressed genes, but also to get these...
Forum: Bioinformatics 09-14-2011, 08:25 AM
Replies: 0
Views: 1,399
Posted By asling
ALIGNED BASES in picard

we have a bam file generated by tophat in out RNA-seq analysis, and CollectAlignmentSummaryMetrics in picard was used to evaluate the mapping quality. Our reads are pair-end, the result shows that...
Forum: Bioinformatics 08-10-2011, 06:09 PM
Replies: 13
Views: 3,775
Posted By asling
hi~I read the paper, and we have used a random...

hi~I read the paper, and we have used a random hexamer to prime the RNA, it seems the most common way to prime the RNA. The author suggest that trimming the sequence at the beginning of the reads...
Forum: Bioinformatics 08-02-2011, 11:53 PM
Replies: 13
Views: 3,775
Posted By asling
Your advice is quite helpful, our FastQC graphs...

Your advice is quite helpful, our FastQC graphs show that the quality scores are declining dramatically especially in the last 15~20 bp region of our reads. So we use fastx_toolkit to cut the low...
Forum: RNA Sequencing 07-27-2011, 12:52 AM
Replies: 0
Views: 2,065
Posted By asling
novel genes and transcripts in cuffdiff output

hi,everyone
We used tophat-cufflink-cuffmerge-cuffcompare-cuffdiff line to detect gene differential expression among samples. The result of cuffdiff shows that there are many new genes and isoforms...
Forum: Bioinformatics 07-25-2011, 09:39 PM
Replies: 13
Views: 3,775
Posted By asling
hi,kmcarr Thanks for your reply! our tophat has...

hi,kmcarr
Thanks for your reply! our tophat has generated 4 different logs named like "bowtie.left_kept_reads_seg1.fixmap.log",do you set any argument so that the repeated time could be higher? what...
Forum: Bioinformatics 07-24-2011, 11:59 PM
Replies: 13
Views: 3,775
Posted By asling
pbluescript and Douglas, thanks for your advice! ...

pbluescript and Douglas, thanks for your advice!
according to your suggestion,i use FastQC to check my reads' quality. the result shows that my reads have big problems on several tests(very...
Forum: Bioinformatics 07-23-2011, 11:37 PM
Replies: 13
Views: 3,775
Posted By asling
we used a pair-end RNA-seq,and the reads length...

we used a pair-end RNA-seq,and the reads length is 90. i don't quite understand what is the 'quality' you refered to. the command line is like:

tophat -r 200 -G /path/to/gtf/dog.gtf -o tophat_dog ...
Forum: Bioinformatics 07-23-2011, 07:12 PM
Replies: 13
Views: 3,775
Posted By asling
strange decreased alignment by tophat

hi,we have conducted RNA_seq mapping and alignment by tophat. Before tophat finished,we monitored the logs for bowtie ,it shows a mapping ratio as below:
# reads processed: 20788750
# reads with at...
Showing results 1 to 14 of 14

 


All times are GMT -8. The time now is 12:55 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO