cole tapnell paper in 2012 describing RNA seq experiment

[ajay87]

hello,

I have been trying to do analysis of RNA seq data, using the protocol given by tapnell paper in 2012 >> http://www.nature.com/nprot/journal/...2012.016.html#

I was trying to build bowtieIndex using command specified in paper
command was..
$ ln –s ./Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BowtieIndex/genome.*. \

bu I am getting error>>
ln: target `./Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BowtieIndex/genome.rev.2.ebwt' is not a directory

Please help me to sort out so that I could run this command

tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq

[GenoMax]

hello,

I have been trying to do analysis of RNA seq data, using the protocol given by tapnell paper in 2012 >> http://www.nature.com/nprot/journal/...2012.016.html#

I was trying to build bowtieIndex using command specified in paper
command was..
$ ln –s ./Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BowtieIndex/genome.*. \

bu I am getting error>>
ln: target `./Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BowtieIndex/genome.rev.2.ebwt' is not a directory

Please help me to sort out so that I could run this command

tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq

There is an extra "\" (highlighted in red and bold above) at the end of your link command. You may need to replace that with a "."

You are not actually "building" the indexes but are only creating a link to the index files you downloaded with the test data in this case.

[ajay87]

Thanks, this problem is solved.

[Histone3]

I'm having the same trouble.

$ ln –s ./Drosophila_melanogaster/Ensembl/BDGP5.25/Sequence/BowtieIndex/genome.*.

link genome.*. is marked red in linux console and I can't run the following command to finish the analysis.

Could anyone explain explicitly how to resolve this?

Even I replace "\" with "." it doesn't work for me.