User: reubenmcgregor88

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Posts by reubenmcgregor88

<prev • 15 results • page 1 of 2 • next >
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Using HTseq and DEseq2 for RNAseq quantitation, format of input data?
... Hi all, For clarities sake my experimental setup is: 2 conditions (treated + non treated), with 3 replicated per condition. This was sequenced using paired end Hiseq. I mapped to reference genome using TopHat2 and counted the reads using htseq-count for all of the alignments separately. I am abo ...
htseq deseq2 rna-seq written 5 months ago by reubenmcgregor8850
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Get fasta file from peak called BED file to do Motif analysis
... Hi all, I have some called peaks in BED format and would like to extract the sequences in a FASTA format in order to do Motif analysis on the regions. I have tried to use the "getfastabed" BEDtool but even though the tool claims to do the following: bedtools getfasta will extract the sequence def ...
fasta motif getfastabed bed bedtool written 7 months ago by reubenmcgregor8850
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Comment: C: Tool dependencies, how to set the value of tool dependencies
... Hi Jen, I reached out to a friend who has used python a lot. And we managed to set the directory and edit the galaxy.ini file. I'm pretty sure it worked because I can now check the "Handle tool dependencies?" box. However now when I trey to install any tool I get an error message: please see pictu ...
written 11 months ago by reubenmcgregor8850
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Comment: C: Tool dependencies, how to set the value of tool dependencies
... Hi again Jen, Sorry I've been asking so many questions, real rookie. On the link it again states "Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of config/galaxy.ini ...
written 11 months ago by reubenmcgregor8850
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Tool dependencies, how to set the value of tool dependencies
... Hi I have just managed to install a local version of galaxy and install it and set myself up as the Admin. I have very limited command line experience so this was a big step for me ;-) I am now trying to install a tool on toolshed and have found it on the main toolshed. However when I get to the i ...
tool_dependency_dir local galaxy admin toolshed written 11 months ago by reubenmcgregor8850 • updated 11 months ago by Jennifer Hillman Jackson22k
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Comment: C: Motif Search from Bed file
... Thanks as always Jen :) ...
written 11 months ago by reubenmcgregor8850
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Comment: C: Motif Search from Bed file
... Hi Jennifer, I used "SeqPos motif tool (version 1.0.0) " in the public "cistrone" at http://cistrome.org/ap/ Hope that makes sense? Cheers ...
written 11 months ago by reubenmcgregor8850
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Motif Search from Bed file
... Hi all, I have recently generated a list of motifs of TF binding sites within peaks of my ChIPseq experiment. However this list tell me how many times the motif is present within my BED file, not where, i.e. which peaks have the motif associated with them. I could take all of the sequences of inte ...
chip-seq motif tool cistrome.org written 11 months ago by reubenmcgregor8850 • updated 11 months ago by Jennifer Hillman Jackson22k
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Comment: C: ChIPseq Peak annotation and downstream analysis
... It's great, just as the there one was thanks, Stupid question, in the tutorial why do you "get flanks" with an offset of 10,000bp? Surely this will only get flanks starting 10,000bp upstream of all the genes? Missing a large portion of upstream sequence that could be promote region? Like I said ma ...
written 11 months ago by reubenmcgregor8850
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Comment: C: ChIPseq Peak annotation and downstream analysis
... Thanks I am using the main instance of galaxy. I have actually used your training to get to the stage I am at. It's a great tutorial, would have been lost without it. I've completed it and used it to map my own reads and look at the data for my "favourite" genes in IGV and it worked great. But ...
written 11 months ago by reubenmcgregor8850

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