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Forum: Bioinformatics 08-11-2015, 05:52 AM
Replies: 2
Views: 704
Posted By anyone1985
I do not know the copies of chromosome. My...

I do not know the copies of chromosome. My subject is Mycobacterium tuberculosis. In the following papers, they used samtools. I will compare the results from gatk and freebayes (haploid model) and...
Forum: Bioinformatics 08-09-2015, 10:31 PM
Replies: 2
Views: 704
Posted By anyone1985
issue about microbial variant detection

I use gatk, freebayes and samtools to calling the variant from microbial sequence. According to the common sense, I think I should use the haploid model like gatk or freebayes. However, several...
Forum: Bioinformatics 07-16-2015, 10:12 PM
Replies: 1
Views: 706
Posted By anyone1985
reads mapping to each strand?

I read some literatures about call sv with samtools and noticed a filter to remove the candidate sv based on the reads mapping to each strand. for example, this paper...
Forum: Bioinformatics 04-19-2012, 03:01 AM
Replies: 1
Views: 1,516
Posted By anyone1985
Problem of New DESeq without any replicates

Recently, I do some RNA-seq analysis. The old version of DESeq do well with the data set without any replicate. However, I came across some error when i ran the newest version following the...
Forum: Bioinformatics 03-22-2012, 09:37 PM
Replies: 0
Views: 1,566
Posted By anyone1985
If orthomcl is right

I have build the ortholog cluster used the orthomcl 2.0. And i found that some clusters has very different protein lengths. For example, some length is 1000aa, some is 300aa. I think some domain in...
Forum: General 11-09-2011, 06:18 AM
Replies: 0
Views: 1,343
Posted By anyone1985
T4 Ligase Bias

Whether T4 DNA ligase’s binding site have preference of GC content,which can induce uneven coverage? Is there some papers related to it?
Forum: Illumina/Solexa 11-09-2011, 06:17 AM
Replies: 0
Views: 2,057
Posted By anyone1985
T4 Ligase Bias

Whether T4 DNA ligase’s binding site have preference of GC content,which can induce uneven coverage? Is there some papers related to it?
Forum: General 08-29-2011, 11:06 PM
Replies: 1
Views: 2,473
Posted By anyone1985
KEGG Mapper Question: what does the red-word black-border boxes mean

There are some red -word black-border boxes in the image from KEGG mapper. I could not find the exact means in the website. I know the red-word red-box is the mapped object. But what does the...
Forum: Bioinformatics 08-19-2011, 04:30 AM
Replies: 6
Views: 3,424
Posted By anyone1985
thanks. I think i know

thanks. I think i know
Forum: Bioinformatics 08-19-2011, 04:19 AM
Replies: 6
Views: 3,424
Posted By anyone1985
usable reads? clean reads? clean reads: the...

usable reads? clean reads?
clean reads: the reads passed the filter
usable reads: maybe the reads mapping to the genome or miRbase
i don't know wheather i am right.
Forum: Bioinformatics 08-19-2011, 02:37 AM
Replies: 6
Views: 3,424
Posted By anyone1985
OK, i see. what standard should i take for the...

OK, i see. what standard should i take for the enough of a miRNA job? Coverage? Number of Reads?
Forum: Bioinformatics 08-18-2011, 09:27 PM
Replies: 6
Views: 3,424
Posted By anyone1985
how many reads is enough in miRNA-seq

I want to do some miRNA-seq of mouse, how many reads from Hiseq is enough for my further research? 10M, 20M or 30M?
Forum: Bioinformatics 12-17-2010, 02:14 AM
Replies: 2
Views: 1,894
Posted By anyone1985
export scaffold or link information

I have got about 189 contigs from velvet by assembling 75 bp pair end sequence. Now, i get some 3k mate pair sequence, and align with the contigs. I'd like to know if there is some software can help...
Forum: Bioinformatics 10-03-2010, 12:12 AM
Replies: 3
Views: 1,620
Posted By anyone1985
you mean velvet can reverse the reads itself,...

you mean velvet can reverse the reads itself, even if it is mate pairs. however, in the mailing list, more than one time, they have mentioned to reverse both of the two reads to assemble the mate...
Forum: Bioinformatics 09-09-2010, 05:26 AM
Replies: 0
Views: 1,348
Posted By anyone1985
Any good idea for assembling 454 and Solexa mate-pair data

New, I am working to assemble 454 (2.9G), Solexa pair-end (insert length = 400bp, read length = 120bp) and mate-pair (insert length = 3K and 5K, read length = 36bp). I have tried many software,...
Forum: Bioinformatics 03-11-2010, 05:50 PM
Replies: 0
Views: 1,378
Posted By anyone1985
Calculate phrap quality with two 3730 reads

I have some 3730 reads, and assemble them with phredPhrap. And I'd like to know how to calculate the final quality?
Forum: Bioinformatics 10-12-2009, 05:15 PM
Replies: 26
Views: 12,997
Posted By anyone1985
Thanks for your help. The author of glimmer has...

Thanks for your help. The author of glimmer has provided me the simplest to compile successful. Chane the line 26 of file delcher.hh in the src/Common directory from
#include <sting> to #include...
Forum: Bioinformatics 10-11-2009, 09:09 AM
Replies: 26
Views: 12,997
Posted By anyone1985
I think i have install the libstdc++6, however,...

I think i have install the libstdc++6, however, the compile still failed. My system is ubuntu, the kernel is
Linux 2.6.27-14-server #1 SMP Tue Jul 7 22:58:31 UTC 2009 x86_64 GNU/Linux, my gcc...
Forum: Bioinformatics 10-09-2009, 06:49 PM
Replies: 26
Views: 12,997
Posted By anyone1985
No, there is no aconfigure script. As the manual,...

No, there is no aconfigure script. As the manual, I have changed the src/common/delcher.hh, or compile in the SimpleMake directory. However, the fatal error always happened.
Forum: Bioinformatics 10-09-2009, 04:40 AM
Replies: 26
Views: 12,997
Posted By anyone1985
Yes, I had compile the maq, velvet successful. I...

Yes, I had compile the maq, velvet successful. I guess missing the core development libraries is not the problem.
Forum: Bioinformatics 10-08-2009, 08:56 PM
Replies: 26
Views: 12,997
Posted By anyone1985
glimmer compile error

When I installed the glimmer3, I came across fatal compile error. Please help me!

bioinfo@bioinfo-desktop:~/software/glimmer3.02/src$ make
* Make Target is all
##### Making Directory ...
Forum: Bioinformatics 09-07-2009, 07:28 PM
Replies: 2
Views: 3,279
Posted By anyone1985
Yes, glimmer with the training data is perfect....

Yes, glimmer with the training data is perfect. However, the contigs are parts of the genome. The training data maybe not suitable for the contig. Or I should do the training for every contig?
Forum: Bioinformatics 09-06-2009, 02:11 AM
Replies: 2
Views: 3,279
Posted By anyone1985
How to use Glimmer to predict orf from Solexa contigs

A genome about 6M has about 340 solexa contigs. I'd like to predict genes of each contig with the Glimmer. I don't know to do it from reference genome as training data or if i can use the long-orf to...
Forum: Bioinformatics 09-06-2009, 12:20 AM
Replies: 1
Views: 1,694
Posted By anyone1985
Unhappy blast puzzle

When I ran the blast with the parameter of "-b 1 -v 1", the result still had several subjects. This puzzle has puzzled me long time.
Forum: Bioinformatics 08-31-2009, 04:35 AM
Replies: 5
Views: 2,588
Posted By anyone1985
Yes, every read. I used the velvet to assemble...

Yes, every read. I used the velvet to assemble the genome. I did not know if it would affect the result of assemble. Whether should I remove the Ns first?
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