SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 14 of 14
Search took 0.00 seconds.
Search: Posts Made By: lei
Forum: Bioinformatics 08-03-2011, 10:33 AM
Replies: 7
Views: 2,275
Posted By lei
OK, I wrote one, but not so fast, that's why I...

OK, I wrote one, but not so fast, that's why I ask here to check whether there is some tool to do it already.
Forum: Bioinformatics 08-03-2011, 10:30 AM
Replies: 4
Views: 2,659
Posted By lei
really?I just got one csfasta and qual file...

really?I just got one csfasta and qual file including 8 libraries from the core facility. If so, I will ask them tomorrow.
Forum: Bioinformatics 08-03-2011, 07:17 AM
Replies: 7
Views: 2,275
Posted By lei
how to trim solid reads length?

are there any tools available to trim solid reads length? for example, I want to extract first 30bp.
Thanks!
Forum: Bioinformatics 08-03-2011, 07:12 AM
Replies: 4
Views: 2,659
Posted By lei
how to separate barcode libraries from csfasta and qual file

anyone knows about how to do that?
Thanks!
Forum: Bioinformatics 04-26-2011, 02:09 PM
Replies: 3
Views: 2,739
Posted By lei
a question about Saturation analysis in MEDIPS

hi,
I am now using MEDIPS for MCIP-seq analysis.
For the Saturation analysis, I don't know how to explain the results. So which value I should focuse in order to answer the question that how many...
Forum: Bioinformatics 04-12-2011, 11:48 PM
Replies: 6
Views: 2,144
Posted By lei
some error message from BFAST match

hi,

I got some error message when I use BFAST for solid data mapping:

error 1:

In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write m->readLength, m->qualLength,...
Forum: RNA Sequencing 03-20-2011, 12:53 PM
Replies: 12
Views: 2,526
Posted By lei
the econd script is : #!/bin/bash #PBS...

the econd script is :

#!/bin/bash

#PBS -N Tophat_lib1
#PBS -l nodes=1:ppn=8:lsdf
#PBS -l walltime=50:00:00
#PBS -l mem=5g
#PBS -M l.gu@gmail.com
#PBS -m ae
Forum: RNA Sequencing 03-20-2011, 12:50 PM
Replies: 12
Views: 2,526
Posted By lei
the first script is : #!/bin/bash #PBS...

the first script is :

#!/bin/bash

#PBS -N Tophat_lib1
#PBS -l nodes=1:ppn=8:lsdf
#PBS -l walltime=50:00:00
#PBS -l mem=5g
#PBS -M l.gu@gmail.com
#PBS -m ae
Forum: RNA Sequencing 03-17-2011, 02:22 AM
Replies: 12
Views: 2,526
Posted By lei
yes, 1),2),3) are all fine. 1) it's possible...

yes, 1),2),3) are all fine.
1) it's possible that the genome fasta file has "chr1" etc. whereas the GTF file has "1" etc. but I ran cuffdiff from the same author successfully with the same GTF file...
Forum: RNA Sequencing 03-14-2011, 04:39 AM
Replies: 12
Views: 2,526
Posted By lei
sure, I runned tophat before with illumina data,...

sure, I runned tophat before with illumina data, everything was fine. those error just happened when I use solid data.
Forum: RNA Sequencing 03-14-2011, 04:23 AM
Replies: 12
Views: 2,526
Posted By lei
It's strange that this time, I can run it with my...

It's strange that this time, I can run it with my previous parameters' order. But still report the same error message: IOError: [Errno 2] No such file or directory:...
Forum: RNA Sequencing 03-14-2011, 04:19 AM
Replies: 12
Views: 2,526
Posted By lei
it was running on a Server, the CPU is 24x 2.3...

it was running on a Server, the CPU is 24x 2.3 GHz, the Memory is 80 GB, and the OS is suse11.0.
I used the human genome from UCSC.
I'm not the root user.
Forum: RNA Sequencing 03-13-2011, 10:54 AM
Replies: 12
Views: 2,526
Posted By lei
Dear seqguy Thanks a lot! I runned the...

Dear seqguy
Thanks a lot!
I runned the command in your order. It started to run, but reported another error:
IOError: [Errno 2] No such file or directory:...
Forum: RNA Sequencing 03-11-2011, 01:19 AM
Replies: 12
Views: 2,526
Posted By lei
a question about tophat

I am using tophap with solid single-end data.
the command line is :
tophat --color --quals -p 8 -o $outdir --library-type fr-secondstrand -G $gtffile hg19 $reads $qual

it reports the error...
Showing results 1 to 14 of 14

 


All times are GMT -8. The time now is 10:10 PM.


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