hi all,
I'm a bit of a noob here. I'm working through some transcriptome data using galaxy and am having a couple troubles.
I have SOLiD data, paired end, but with the F5-BC tag. I have watched the screencast on the galaxy page which says that solid mapping for paired ends has reads that go the same direction, but the SOLiD F5-BC tag actually goes the opposite direction apparently. So, question 1: can galaxy figure this out?
Next, I've done a trial run with this data and gone through to cuffcompare without problems although I couldn't get cuffdiff to run within galaxy. No biggie, though because I could run it in the terminal. Sweet. But I have a question about the output. When I look at the gene expression file, in sample1 and sample2 columns there are codes ranging from q1-q5. What do these mean? I'm only comparing one sample with another sample and don't really get what is going on here.
Any advice would be greatly appreciated.
S
I'm a bit of a noob here. I'm working through some transcriptome data using galaxy and am having a couple troubles.
I have SOLiD data, paired end, but with the F5-BC tag. I have watched the screencast on the galaxy page which says that solid mapping for paired ends has reads that go the same direction, but the SOLiD F5-BC tag actually goes the opposite direction apparently. So, question 1: can galaxy figure this out?
Next, I've done a trial run with this data and gone through to cuffcompare without problems although I couldn't get cuffdiff to run within galaxy. No biggie, though because I could run it in the terminal. Sweet. But I have a question about the output. When I look at the gene expression file, in sample1 and sample2 columns there are codes ranging from q1-q5. What do these mean? I'm only comparing one sample with another sample and don't really get what is going on here.
Any advice would be greatly appreciated.
S
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