User: benjyrolls

gravatar for benjyrolls
benjyrolls10
Reputation:
10
Status:
New User
Location:
Last seen:
16 hours ago
Joined:
2 months, 1 week ago
Email:
b*********@gmail.com

Posts by benjyrolls

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
109
views
1
answers
Comment: C: Upstream Regulator Gene Differential expression
... As per you statement "Checking for known binding sites in the majority of the DE genes should reasonably suffice for this." I have performed a check on the binding sites and this is what I [found][1] Sox2 seems to be regulating some genes in conjunction with others? [1]: http://159.149.160.88 ...
written 3 days ago by benjyrolls10
0
votes
1
answer
109
views
1
answers
Comment: C: Upstream Regulator Gene Differential expression
... There are 3 replicates. Well, I was trying to reproduce the results in [this experiment][1] using the RNA-Seq data however am not confident in the differentially expressed genes and its role to Sox2 in terms of RNA-Seq. However in the ChIp-Seq experiment, Centrimo motif analysis, using the Chip-Se ...
written 4 days ago by benjyrolls10
0
votes
1
answer
109
views
1
answers
Comment: C: Upstream Regulator Gene Differential expression
... Well am very new to RNA Seq because I have a wild type mouse with Sox2 injected(condition 1) and other with SoX2 removed(condition 2) I was thinking the differentially expressed gene will be as a result of Sox2? Can I say that Sox2 presence is driving the response and the DE genes are as a result o ...
written 4 days ago by benjyrolls10
5
votes
1
answer
109
views
1
answer
Upstream Regulator Gene Differential expression
... Hi I performed an RNA Seq on two conditions SOX2 WT mouse and SOX2 KO mouse to find the genes which were differentiallly expressed through an RNA Seq pipeline and eventually obtained the differentially expresses DE genes by Cuffdiff To find the upstream regulators these differentially observed ge ...
rna-seq written 4 days ago by benjyrolls10
0
votes
0
answers
61
views
0
answers
Empty Cuffdiif Output except Gene Differential expression testing
... Hello I am running a Cuffdiff on two separate conditions of a file. all outputs seem to be empty except the gene differential expression output which shows the deferentially expressed genes. does it mean this output is wrong. i have followed other similar outputs on the forum but cant get this t ...
galaxy cuffdiff rna-seq written 5 days ago by benjyrolls10
0
votes
1
answer
110
views
1
answer
Finding Gene names from chromosome positions whilst maintaining fold change and p and q values
... hi I have a peaks interval output from MACS2.1 which is attached below. How do I find the gene names using the start and end positions, whilst maintaining the fold change values in Galaxy in my file attached below? I have followed other posts on the forum such as [this one][1] but this does retur ...
macs galaxy chip-seq written 14 days ago by benjyrolls10 • updated 14 days ago by Devon Ryan64k
0
votes
1
answer
154
views
1
answers
Comment: C: Ingenuity Pathway Analysis Galaxy Dataset
... Thanks I have the negative and positive peaks now. Is it advisable to add some bases to the left and right from the peaks summits file, as its normally done in discovering motiffs, which files to use here the peaks interval for GeneSCF? MACS2 provides gene ids in RefSeq form? Will GeneSCF work on Wi ...
written 16 days ago by benjyrolls10
0
votes
1
answer
154
views
1
answers
Comment: C: Ingenuity Pathway Analysis Galaxy Dataset
... Thanks for the Reply. I have these output from MACS2.1 1. (treat pileup: bedGraph) 2. (peaks: interval) 3. (peaks: narrowPeak) 4. (summits: bed) 5. (control lambda: bedGraph) 6. (treat pileup: bigWig) so I havent got the negative and positive peaks. How do I get these negative and positive pe ...
written 17 days ago by benjyrolls10
4
votes
1
answer
154
views
1
answer
Ingenuity Pathway Analysis Galaxy Dataset
... Hi I have a MACS output from a ChIP-Seq experiment, could someone explain how I can find the processes which are down or up regulated using my peaks interval file. I have used GREAT but am only able to find genes and a few processes which are enriched. Secondly I have Ingenuity Pathway Analysis ...
chip-seq macs2 cuffdiff ipa rna-seq written 17 days ago by benjyrolls10
0
votes
1
answer
111
views
1
answers
Comment: C: MACS2 Output for GREAT
... Am using galaxy is there a way to do this? ...
written 28 days ago by benjyrolls10

Latest awards to benjyrolls

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1808 users visited in the last hour