SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 10 of 10
Search took 0.00 seconds.
Search: Posts Made By: dingkai0564
Forum: Bioinformatics 08-31-2011, 09:27 PM
Replies: 6
Views: 3,408
Posted By dingkai0564
how to use mira to assemble the fastq generated by 454 sequencing

Hi;

I have some questions to use MIRA: I am asking for help about how to use the mira to assemble my fastq file

I had downloaded the fastq file I am interested from NCBI SRA database. But It...
Forum: RNA Sequencing 08-31-2011, 09:25 PM
Replies: 0
Views: 1,573
Posted By dingkai0564
Red face How to use MIRA to assemble 454 fastaq file alone

Hi;

I have some questions to use MIRA: I am asking for help about how to use the mira to assemble my fastq file

I had downloaded the fastq file I am interested from NCBI SRA database. But It...
Forum: 454 Pyrosequencing 08-29-2011, 12:01 AM
Replies: 2
Views: 1,801
Posted By dingkai0564
Yes, I am trying to use mira to do my work!...

Yes, I am trying to use mira to do my work! thanks for your good advice.

The reason why I want to post here is that I still want to solve the problem because it is still there.

But I think...
Forum: 454 Pyrosequencing 08-25-2011, 01:37 AM
Replies: 2
Views: 1,801
Posted By dingkai0564
problems when using the software Phrap and consed

when I use consed to display ace file generated by phrap one error happens:

The error is :

exception thrown: ace file error detected from source file parseAceFile.cpp at 2368
Error in file...
Forum: Bioinformatics 08-25-2011, 12:05 AM
Replies: 0
Views: 1,419
Posted By dingkai0564
something wrong when using consed

when I use consed to display ace file generated by phrap one error happens:

The error is :

exception thrown: ace file error detected from source file parseAceFile.cpp at 2368
Error in file...
Forum: Bioinformatics 11-10-2010, 06:33 PM
Replies: 1
Views: 1,872
Posted By dingkai0564
the tophat generate the bam file instead of sam files?

I have a question:

when i trying to use tophat (to alignment in order to generate the SAM file when can be loaded into the cufflinks.Why the output only gives me bam files in the default...
Forum: Bioinformatics 11-05-2010, 01:24 PM
Replies: 5
Views: 2,460
Posted By dingkai0564
Thank you all! i solve the problems.

Thank you all! i solve the problems.
Forum: Bioinformatics 11-05-2010, 09:56 AM
Replies: 5
Views: 2,460
Posted By dingkai0564
About the HTseq

Thanks for your advice. It seems that i can make the HTseq running,however,i only get the results of :

50972 GFF lines processed.
100000 reads processed.
200000 reads processed.
300000 reads...
Forum: Bioinformatics 11-04-2010, 09:40 PM
Replies: 5
Views: 2,460
Posted By dingkai0564
asking questions about gtf files

we are using bowtie to generate the bam file.we are intend to use tophat and cufflink ,HTseq to count the short reads.but we can not find any gtf file related to our species.Could we use these...
Forum: RNA Sequencing 11-04-2010, 05:19 PM
Replies: 0
Views: 1,427
Posted By dingkai0564
looking for solution to count the short reads in rice

recently i am analyzing the RNA-seq in rice.However,when i want to use tophat or HTseq to analysis my illumina data, it seems that it need GTF file.However, I only have the GFF3 file.Could anybody...
Showing results 1 to 10 of 10

 


All times are GMT -8. The time now is 07:37 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO