Re: [galaxy-user] Barcode splitter on paired end data

Dear Dr. Jennifer,   Thank you very much for the reply. I am sorry about the way the thread was handled. Your input is much helpful. However, I have one key question which probably didnt come across well in the third question and I will try to re-word it. I am using Illumina paired end data and

Re: [galaxy-user] Parameters for merging BAM files

Hi Jen, Thanks for the information. I used this setting and the merged BAM files (.accepted hits) worked quite well for the downstream analysis. Best, Jianguang From: Jennifer Jackson [j...@bx.psu.edu] Sent: Tuesday, April 09, 2013 4:10 PM To: Du, Jianguang Cc:

Re: [galaxy-user] Are reads of 36nt in length long enough to accutatly map on splicing junctions?

Hi Jeremy, Thank you very much for the reply. I have some more questions of the same topic. 1) My reads are 36nt long. How much should I set for "the Minimum length of reads segments" to get the most reliable output with the highest mapping of splicing junctions?. In my previous run of TopHat

Re: [galaxy-user] merging fastq files

Dear Jen. Yes, that was my problem, I skipped some steps by relying too much on the screencast and ignoring the text. Now I am reluctant to launch the AMI as I having trouble estimating my usage and costs on AWS - as a new user I have little idea what to set many of the parameters in the usage c

Re: [galaxy-user] Are reads of 36nt in length long enough to accutatly map on splicing junctions?

> 1) My reads are 36nt long. How much should I set for "the Minimum length of > reads segments" to get the most reliable output with the highest mapping of > splicing junctions?. In my previous run of TopHat, I set it as 18. Can I > reduce it more to get better mapping on splicing junctions? Yo

Re: [galaxy-user] merging fastq files

Hi Andrew, We do not have any estimates posted on the wiki currently for example usage on the cloud, but this is a good idea and the team is discussing the best way to add in something like this. The difficulty comes with how variable actual job run-times can be, but there still are some ways

Re: [galaxy-user] Are reads of 36nt in length long enough to accutatly map on splicing junctions?

> I have one more question about the "Anchor length". For a RNA-seq read mapped > on the splicing junction under the 0 mismatch condition, if 5 nucleotides of > one end map on one exon, does it mean the rest part of the read must map on > the adjacent exon? What I want to understand is that, al