Hi everyone,
I've been going through the Nature protocol paper, manuals, and this forum for the tuxedo protocol (tophat, cufflinks, cuffmerge, cuffidff, etc.) and for cummeRbund and I think I have most things sorted out.
I ran everything with the public Galaxy server, and got the 15 tabular and 1 gtf (from cuffmerge) file results. I imported everything into R/cummeRbund via the code from http://seqanswers.com/forums/showthread.php?t=31622 (though I should note that while the original poster for that thread seemed to have problems with their code, I didn't have many problems) and everything seems fine... until I try to do/see anything related to replicates.
My resulting database only shows 1 sample per condition in cummeRbund. I have tried to make sure all the read groups fields have been filled in in Tophat2 and cuffdiff was set to "Yes" for exporting read group data. I use the most updated version of all program in usegalaxy (like tophat2, etc.), and R 3.1.2 and cummeRbund is also fairly up to date I think (I installed everything about a month or two ago). I just wanted to know, has anyone else been able to get replicates to display properly in R from usegalaxy data?
Thank you all very much!
YXC
P.S: just thought I should list a few things I've considered might be pertinent information for anyone trying to help me:
1) there was a thread mentioning that sample groups' id's shouldn't start with numbers and shouldn't have non-alpha-numeric symbols in them - I have followed this instruction, but when I look at one of the read group tracking files (output from cuffdiff), it lists replicates as 0, 1, or 2... could this be the problem?
2) some people have also in related threads mentioned something about sqlite server issues? I have no idea what this really means to be honest. I did read in the manual that to install cummeRbund we need sqlite server and I've downloaded an executable binary for it... but when I double click it I just get what seems to be a dos window and R/cummeRbund works without me doing anything with sqlite... I am confused to the role/use of sqlite, and whether it's even related to my problem?
thank you again in advance, to everyone
I've been going through the Nature protocol paper, manuals, and this forum for the tuxedo protocol (tophat, cufflinks, cuffmerge, cuffidff, etc.) and for cummeRbund and I think I have most things sorted out.
I ran everything with the public Galaxy server, and got the 15 tabular and 1 gtf (from cuffmerge) file results. I imported everything into R/cummeRbund via the code from http://seqanswers.com/forums/showthread.php?t=31622 (though I should note that while the original poster for that thread seemed to have problems with their code, I didn't have many problems) and everything seems fine... until I try to do/see anything related to replicates.
My resulting database only shows 1 sample per condition in cummeRbund. I have tried to make sure all the read groups fields have been filled in in Tophat2 and cuffdiff was set to "Yes" for exporting read group data. I use the most updated version of all program in usegalaxy (like tophat2, etc.), and R 3.1.2 and cummeRbund is also fairly up to date I think (I installed everything about a month or two ago). I just wanted to know, has anyone else been able to get replicates to display properly in R from usegalaxy data?
Thank you all very much!
YXC
P.S: just thought I should list a few things I've considered might be pertinent information for anyone trying to help me:
1) there was a thread mentioning that sample groups' id's shouldn't start with numbers and shouldn't have non-alpha-numeric symbols in them - I have followed this instruction, but when I look at one of the read group tracking files (output from cuffdiff), it lists replicates as 0, 1, or 2... could this be the problem?
2) some people have also in related threads mentioned something about sqlite server issues? I have no idea what this really means to be honest. I did read in the manual that to install cummeRbund we need sqlite server and I've downloaded an executable binary for it... but when I double click it I just get what seems to be a dos window and R/cummeRbund works without me doing anything with sqlite... I am confused to the role/use of sqlite, and whether it's even related to my problem?
thank you again in advance, to everyone
