Forum: Academic/Non-Profit Jobs
02-05-2021, 01:17 PM
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Replies: 0
Views: 338
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Forum: Academic/Non-Profit Jobs
02-03-2021, 12:14 PM
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Replies: 0
Views: 219
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Forum: Academic/Non-Profit Jobs
01-02-2020, 07:08 AM
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Replies: 0
Views: 1,105
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Forum: Bioinformatics
12-06-2018, 05:38 AM
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Replies: 678
Views: 214,573
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Forum: Bioinformatics
12-05-2018, 07:42 AM
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Replies: 0
Views: 1,487
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Forum: Illumina/Solexa
09-12-2017, 07:25 AM
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Replies: 4
Views: 1,778
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Forum: Illumina/Solexa
09-12-2017, 05:53 AM
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Replies: 4
Views: 1,778
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Forum: Illumina/Solexa
09-11-2017, 01:16 PM
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Replies: 4
Views: 1,778
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Forum: Bioinformatics
09-01-2014, 07:41 AM
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Replies: 0
Views: 1,759
Is BQSR necessary for de novo mutation calling?
Hi there,
I have been using GATK to identify variants recently. I saw that BQSR is highly recommended. But I don’t whether it is still needed for de novo mutation calling. For example, I want to...
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Forum: Epigenetics
03-03-2014, 04:57 PM
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Replies: 1
Views: 2,025
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Forum: Genomic Resequencing
11-29-2012, 07:37 PM
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Replies: 0
Views: 2,673
Problems when calling SNPs using samtools mpileup
Hi there,
Recently, I'm using samtools mpileup to call SNPs using low coverage (average 1x) resequencing data of 600+ populations. But I encountered a few problems.
My command line is as follows:...
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Forum: Bioinformatics
10-08-2012, 09:10 PM
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Replies: 13
Views: 9,204
How did you handle this problem?
Hi vinila86,
Recently I have enconter the same problem. I want to know how did you handle this problem finally.
I have used sra-dbcc to check the file, and the report was as follows:...
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Forum: RNA Sequencing
11-02-2011, 11:33 PM
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Replies: 0
Views: 1,235
Cuffdiff:bug or misunderstanding
Hi there,
Recently, I'm using tophat and cufflinks to processing RNA -seq data.When I checked the cuffdiff results, I saw that if PRKM one of the sample was 0 then, then value of significant would...
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Forum: RNA Sequencing
10-17-2011, 11:36 PM
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Replies: 4
Views: 4,475
Thanks for your help
Now I know all of results of the comparisons betweem pairs are saved in one file.
Thanks!
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Forum: RNA Sequencing
10-17-2011, 05:49 PM
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Replies: 4
Views: 4,475
I have checked the outpu directory.
In fact, I have checked the outpu directory, and there are only 11 files as follows:cds.diff , cds_exp.diff,genes.fpkm_tracking, isoforms.fpkm_tracking ,splicing.diff, tss_groups.fpkm_tracking ,...
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Forum: RNA Sequencing
10-17-2011, 02:37 AM
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Replies: 2
Views: 3,045
For question 1, did you use an annotation in...
For question 1, did you use an annotation in cufflinks or cuffcompare? If so ,I thinks this might explain this:
Cuffdiff and Cufflinks now accept new options controlling whether all hits are...
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Forum: RNA Sequencing
10-17-2011, 01:54 AM
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Replies: 4
Views: 4,475
Cuffdiff with more than two samples
Recently,I'm using Cufflinks to process my RNA-seq data,and I have 4 tissues(more than two).In the mannual of cuffdiff,you said,if more than two are provided, Cuffdiff tests for differential...
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Forum: Bioinformatics
07-12-2011, 07:46 PM
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Replies: 6
Views: 8,741
Questions on the updated illumina quality score
The quality of my datum from an updated illumina system is sanger/illumina 1.9 which confused me very much.Could I just treated them as sanger format?
Can somebody familiar with this can give me...
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Forum: RNA Sequencing
07-10-2011, 05:58 PM
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Replies: 6
Views: 8,648
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Forum: Bioinformatics
06-28-2011, 01:47 AM
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Replies: 31
Views: 19,078
No mismatch allowed
What I want is to dissect the correlation between smRNA and DNA methylation.Previous studies reveals that both of miRNA and siRNA involed in DNA methylation.The problem I met is...
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Forum: Bioinformatics
06-27-2011, 11:07 PM
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Replies: 31
Views: 19,078
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Forum: Bioinformatics
06-22-2011, 01:48 AM
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Replies: 1
Views: 1,621
Ask some help on smRNA analyes
Hi there,
I'm new to smRNA analyes,and I didn't get some satisfied pileline.
I have sequenced two adjacent tissues A and B.
And what I want is to identify the smRNA targets,smRNA genes, A-specific...
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Forum: Bioinformatics
05-04-2011, 07:19 PM
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Replies: 648
Views: 192,695
Why not -p option for Bismark
I got the same query,and Felix,Bismark developer,gave a explanation about this,the details are as follows
++++++++++++++++++++++++++++++++++++++++++++++
Let's say you give each of the bowtie...
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Forum: Bioinformatics
04-15-2011, 02:44 AM
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Replies: 648
Views: 192,695
Report from bismark mapping
Hi Felix,
The two attachments are bismark mapping report for a PE and SE lane respectively,and the fastqC report will be emailed to you because of its file size.
The raw reads' length is 100bp...
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Forum: Bioinformatics
04-15-2011, 01:18 AM
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Replies: 648
Views: 192,695
Hey guys,
Recently ,I was using bismark to...
Hey guys,
Recently ,I was using bismark to process my methyC-seq data, but the efficiency of mapping is not so good.And I know the species I work on is transposon rich which is greter than 60%.In...
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