Forum: Core Facilities
12-16-2011, 05:38 AM
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Replies: 7
Views: 4,076
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Forum: Core Facilities
12-14-2011, 11:06 PM
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Replies: 7
Views: 4,076
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...
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Forum: Bioinformatics
12-14-2011, 07:30 AM
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Replies: 0
Views: 2,581
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...
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Forum: Core Facilities
12-14-2011, 07:22 AM
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Replies: 7
Views: 4,076
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...
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Forum: Bioinformatics
12-11-2011, 11:21 PM
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Replies: 6
Views: 3,916
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Forum: Bioinformatics
12-09-2011, 03:54 AM
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Replies: 6
Views: 3,916
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...
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Forum: Bioinformatics
09-14-2011, 08:25 AM
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Replies: 0
Views: 1,399
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...
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Forum: Bioinformatics
08-10-2011, 06:09 PM
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Replies: 13
Views: 3,775
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...
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Forum: Bioinformatics
08-02-2011, 11:53 PM
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Replies: 13
Views: 3,775
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Forum: RNA Sequencing
07-27-2011, 12:52 AM
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Replies: 0
Views: 2,065
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...
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Forum: Bioinformatics
07-25-2011, 09:39 PM
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Replies: 13
Views: 3,775
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...
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Forum: Bioinformatics
07-24-2011, 11:59 PM
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Replies: 13
Views: 3,775
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Forum: Bioinformatics
07-23-2011, 11:37 PM
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Replies: 13
Views: 3,775
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 ...
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Forum: Bioinformatics
07-23-2011, 07:12 PM
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Replies: 13
Views: 3,775
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...
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