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Forum: Bioinformatics 08-08-2017, 06:53 AM
Replies: 648
Views: 193,098
Posted By twotwo
Thanks fkrueger!

Thanks fkrueger!
Forum: Bioinformatics 08-07-2017, 02:30 PM
Replies: 648
Views: 193,098
Posted By twotwo
Hi, fkrueger, Is there any annotation file for...

Hi, fkrueger,
Is there any annotation file for the methylation data? Like after I do the alignment, I can get a probe like: chr, start position.... How can I know which gene is it from? Thank you.
Forum: Bioinformatics 07-27-2017, 01:27 PM
Replies: 648
Views: 193,098
Posted By twotwo
Hi, fkrueger, If I want to compare paired...

Hi, fkrueger,
If I want to compare paired sample (one vs one). Can I do it with seqmonk in unix? Like using some unix command, and obtain a table with p-value per probe?
Forum: Bioinformatics 05-27-2017, 08:41 AM
Replies: 0
Views: 788
Posted By twotwo
question about impute2

Hi, I ran a impute2 command and get the following summary and the running stopped. no output file.

impute2 -known_haps_g chr10.haps -h 1000GP_Phase3_chr10.hap -l 1000GP_Phase3_chr10.legend -m...
Forum: Bioinformatics 05-12-2017, 01:43 PM
Replies: 648
Views: 193,098
Posted By twotwo
Thank you very much!

Thank you very much!
Forum: Bioinformatics 05-12-2017, 11:03 AM
Replies: 648
Views: 193,098
Posted By twotwo
Hi, Felix, Thanks for your quick answer. Here...

Hi, Felix,
Thanks for your quick answer. Here is the head of the coverage file. Does that mean that I should merge the data (get all the information for one SNP) and get the methylation...
Forum: Bioinformatics 05-12-2017, 08:04 AM
Replies: 648
Views: 193,098
Posted By twotwo
Hi, Thanks fkrueger! I ran your code. The...

Hi, Thanks fkrueger! I ran your code. The following is the head what I have from the bedgraph file:

track type=bedGraph
chr11 110189 110190 100
chr11 110211 110212 100
chr11 113464 ...
Forum: Bioinformatics 05-11-2017, 02:39 PM
Replies: 648
Views: 193,098
Posted By twotwo
I have the same question as yours. Did you solve...

I have the same question as yours. Did you solve your problem? Then which command should I use the generate the methylation percentage?
Forum: Bioinformatics 01-14-2014, 06:54 AM
Replies: 7
Views: 1,841
Posted By twotwo
Hi, I used HTseq from python. First you need...

Hi,
I used HTseq from python. First you need to install python, then HTseq.... Just follow the instruction.
Forum: Bioinformatics 01-13-2014, 07:54 AM
Replies: 2
Views: 1,618
Posted By twotwo
Obtain the gene names for FPKM generated from cufflinks command

Hi,
I used the cufflinks command to generate the FPKM values. However, the genes.fpkm_tracking, which have the FPKM values, did not have the gene names. The following is my command.
cufflinks -o...
Forum: Bioinformatics 08-02-2013, 01:15 PM
Replies: 3
Views: 2,213
Posted By twotwo
Hi, First you need to make sure that the...

Hi,
First you need to make sure that the samtools have two folders: /lib and /include
Second, you need to run the configure command like the following. You need have LIBS option. Please let me...
Forum: RNA Sequencing 07-26-2013, 11:27 AM
Replies: 0
Views: 1,660
Posted By twotwo
cuffdiff output problem: what is the value_1 in gene_exp.diff

Hi,
My cuffdiff code is:
cuffdiff -o /path/output /path/reference.gtf group1_1.bam,group1_2.bam group2_1.bam,group2_2.bam

In the output file "gene_exp.diff", I found value_1 and value_2. Is...
Forum: Bioinformatics 07-17-2013, 12:54 PM
Replies: 6
Views: 4,910
Posted By twotwo
great! Thanks! Here is my code. It really...

great! Thanks!
Here is my code. It really works.
./configure LIBS=-lrt --prefix=/home/twotwo/software/tophat209 --with-boost=/home/twotwo/software/boost_154...
Forum: Bioinformatics 07-17-2013, 12:22 PM
Replies: 6
Views: 4,910
Posted By twotwo
Hi, I installed the newest tophat 2.0.9. And I...

Hi, I installed the newest tophat 2.0.9. And I have similar problem in configure.


-- tophat 2.0.9 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2...
Forum: Bioinformatics 07-15-2013, 08:55 AM
Replies: 13
Views: 11,198
Posted By twotwo
Hi, Bob, After I ran this job for another time....

Hi, Bob,
After I ran this job for another time. There is no error message like before. However the result is still confusing. There is only 3 rows in the gene_exp.diff file. The first part of...
Forum: Bioinformatics 07-15-2013, 08:38 AM
Replies: 0
Views: 990
Posted By twotwo
cuffdiff problems: only got 3 records in the gene_exp.diff file

Hi,
I set up a cuffdiff running. Here is my code:
cuffdiff -o /home/twotwo /home/twotwo/reference.gtf {samples from group1 separated by comma}{space}{samples from group2 separated by comma}
...
Forum: Bioinformatics 07-09-2013, 07:06 AM
Replies: 13
Views: 11,198
Posted By twotwo
Thanks so much! I will try that.

Thanks so much! I will try that.
Forum: Bioinformatics 07-08-2013, 11:30 AM
Replies: 13
Views: 11,198
Posted By twotwo
Hi, I have some problem with the cuffdiff...

Hi,
I have some problem with the cuffdiff running. I run the cuffdiff for two conditions (13 samples vs. 8 samples) with the following code:

cuffdiff -o /path/result /path/reference.gtf...
Forum: Bioinformatics 07-05-2013, 10:31 AM
Replies: 2
Views: 1,884
Posted By twotwo
Thanks so much!

Thanks so much!
Forum: Bioinformatics 07-05-2013, 08:42 AM
Replies: 2
Views: 1,884
Posted By twotwo
Samtools sort problem

Hi,
I have bam file from tophat. And I want to sort it, and finally use HTSEq to generate the count file.
Here is my code:
samtools -n my.bam my_sort

After I ran it, it kept generating...
Forum: Bioinformatics 06-24-2013, 01:56 PM
Replies: 84
Views: 27,632
Posted By twotwo
never mind my other reply. When I changed...

never mind my other reply. When I changed address-model from underscore to hyphen, the three options worked!!! Thank you so much!!! I felt much better.
Forum: Bioinformatics 06-24-2013, 01:12 PM
Replies: 84
Views: 27,632
Posted By twotwo
Thanks for being so helpful! Yes, I did not...

Thanks for being so helpful! Yes, I did not update my tophat since I already have my SAM files. Should I update the tophat if I only want to run cuffdiff?
And if I used
1. ./bootstrap.sh
2....
Forum: Bioinformatics 06-24-2013, 10:55 AM
Replies: 84
Views: 27,632
Posted By twotwo
The OS is the linux. And I removed some of the...

The OS is the linux. And I removed some of the option:
bjam --prefix=/home/twotwo/software/boost153/ link=static runtime-link=static stage install
Then it works. Can I install without the option...
Forum: Bioinformatics 06-24-2013, 10:17 AM
Replies: 84
Views: 27,632
Posted By twotwo
Thanks for replying so quick! bjam...

Thanks for replying so quick!
bjam --prefix=/home/twotwo/software/boost153 --toolset=gcc architecture=x86 address_model=64 link=static runtime-link=static stage install


And I got the following...
Forum: Bioinformatics 06-24-2013, 08:31 AM
Replies: 84
Views: 27,632
Posted By twotwo
I have the same problem. Any comments???

I have the same problem. Any comments???
Showing results 1 to 25 of 40

 


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