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Forum: Bioinformatics 12-06-2018, 05:38 AM
Replies: 674
Views: 175,247
Posted By zeam
Hi Brain, could you please answer my questions...

Hi Brain, could you please answer my questions posted here at your convenience? http://seqanswers.com/forums/showthread.php?t=85967

Thanks in advance.
Forum: Bioinformatics 12-05-2018, 07:42 AM
Replies: 0
Views: 789
Posted By zeam
Meanings of "MB" in unambiguousMB generated by BBmap

Hi, I'm using BBmap to do the alignments. In the statistics file, there are "unambiguousMB" and "ambiguousMB". Could somebody explain what "MB" means here? I tried to get help in the manual. But no...
Forum: Illumina/Solexa 09-12-2017, 07:25 AM
Replies: 4
Views: 1,294
Posted By zeam
Thank you, Phillip.

Thank you, Phillip.
Forum: Illumina/Solexa 09-12-2017, 05:53 AM
Replies: 4
Views: 1,294
Posted By zeam
Thank you@nucacidhunter!

Thank you@nucacidhunter!
Forum: Illumina/Solexa 09-11-2017, 01:16 PM
Replies: 4
Views: 1,294
Posted By zeam
what percentage range is normal for undetermined reads in a lane?

Hi,

In the demultiplexed results, there are some undetermined reads. I saw there is one lane that 53% 'of the raw clusters per lane' were undetermined. I'm surprised of this high percentage.
...
Forum: Bioinformatics 09-01-2014, 07:41 AM
Replies: 0
Views: 1,471
Posted By zeam
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 donít whether it is still needed for de novo mutation calling. For example, I want to...
Forum: Epigenetics 03-03-2014, 04:57 PM
Replies: 1
Views: 1,792
Posted By zeam
Have you got any idea for this?

Hi there,
I encounter the same problem with you. I don't whether you had any idea for this problem.
Best.
Forum: Genomic Resequencing 11-29-2012, 07:37 PM
Replies: 0
Views: 2,292
Posted By zeam
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:...
Forum: Bioinformatics 10-08-2012, 09:10 PM
Replies: 13
Views: 8,594
Posted By zeam
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:...
Forum: RNA Sequencing 11-02-2011, 11:33 PM
Replies: 0
Views: 1,093
Posted By zeam
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...
Forum: RNA Sequencing 10-17-2011, 11:36 PM
Replies: 4
Views: 4,073
Posted By zeam
Thanks for your help

Now I know all of results of the comparisons betweem pairs are saved in one file.
Thanks!
Forum: RNA Sequencing 10-17-2011, 05:49 PM
Replies: 4
Views: 4,073
Posted By zeam
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 ,...
Forum: RNA Sequencing 10-17-2011, 02:37 AM
Replies: 2
Views: 2,830
Posted By zeam
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...
Forum: RNA Sequencing 10-17-2011, 01:54 AM
Replies: 4
Views: 4,073
Posted By zeam
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...
Forum: Bioinformatics 07-12-2011, 07:46 PM
Replies: 6
Views: 8,215
Posted By zeam
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...
Forum: RNA Sequencing 07-10-2011, 05:58 PM
Replies: 6
Views: 8,060
Posted By zeam
How to define a expressed gene based on RNA-seq data

Recently,I have been working with RNA-seq data,and one problem I met is how to define a expressed gene.I use RPKM to nomalize the expression level,but the cutoff value to define a expressed gene is a...
Forum: Bioinformatics 06-28-2011, 01:47 AM
Replies: 31
Views: 17,579
Posted By zeam
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...
Forum: Bioinformatics 06-27-2011, 11:07 PM
Replies: 31
Views: 17,579
Posted By zeam
Hi everyone, When you were processing smRNA-seq...

Hi everyone,
When you were processing smRNA-seq data,which software did you use?I have attempted SOAP2 and bowtie,both of them didn't work well enough,many of the reads could not map to the...
Forum: Bioinformatics 06-22-2011, 01:48 AM
Replies: 1
Views: 1,439
Posted By zeam
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...
Forum: Bioinformatics 05-04-2011, 07:19 PM
Replies: 649
Views: 172,278
Posted By zeam
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...
Forum: Bioinformatics 04-15-2011, 02:44 AM
Replies: 649
Views: 172,278
Posted By zeam
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...
Forum: Bioinformatics 04-15-2011, 01:18 AM
Replies: 649
Views: 172,278
Posted By zeam
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...
Forum: Bioinformatics 03-24-2011, 07:41 PM
Replies: 649
Views: 172,278
Posted By zeam
A query on bismark read trimming

Hi Felix,

I have noticed that the bismark didn't have a parameter for read trimming like bwa.If I need read trimming,am I use another tool or bismark have this function that I didn't see?

Best...
Forum: Bioinformatics 03-16-2011, 07:12 PM
Replies: 649
Views: 172,278
Posted By zeam
Queries on Bismark

Hi,felix,

Recently,I have been using the Bismark,Thanks for your wonderful program.

There is something confused me:
1)In the user'guide,I only saw option to handle mismatch of the seed,but...
Forum: Bioinformatics 03-16-2011, 12:29 AM
Replies: 649
Views: 172,278
Posted By zeam
Hi,Oliver, You are right about the SRA...

Hi,Oliver,
You are right about the SRA name,thanks for your replying,and I just think you should let the users know how to modify your script when dealing with SRA data.

Best wishes,
Zeam
Showing results 1 to 25 of 37

 


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