User: sandKings

gravatar for sandKings
sandKings10
Reputation:
10
Status:
New User
Location:
Last seen:
4 weeks, 1 day ago
Joined:
10 months ago
Email:
m**********@gmail.com

Posts by sandKings

<prev • 34 results • page 1 of 4 • next >
0
votes
0
answers
201
views
0
answers
Comment: C: Homer findmotifs.pl keeps failing because it can't find the promoter set which i
... I tried it just now and I got a different error: Selected Options: Input file = /projects/b1042/SKlab/MSC_TPA_project/homer/LPep.txt Promoter Set = mouse Output Directory = /projects/b1042/SKlab/MSC_TPA_project/homer/LPEP/ Modifying analysis for RNA analysis Motif lengt ...
written 8 weeks ago by sandKings10
0
votes
0
answers
201
views
0
answers
Comment: C: Homer findmotifs.pl keeps failing because it can't find the promoter set which i
... None of the options work at all. We've tried mm10, mm9, mouse-p, mouse-o but they all generate the same error stating that the component isn't available. We've even tried to export path to all the folders within Homer but that didn't help either. export PATH=$PATH:/projects/p30120/software/hom ...
written 8 weeks ago by sandKings10
0
votes
0
answers
201
views
0
answers
Homer findmotifs.pl keeps failing because it can't find the promoter set which is installed
... A colleague of mine who's a molecular biologist too and doesn't know bioinformatics at all has been trying to run findmotifs.pl as explained on this [page][1] without any success. Following the syntx: findMotifsGenome.pl -size # [options] She is submitting the following command: /so ...
homer findmotifs.pl written 8 weeks ago by sandKings10
0
votes
2
answers
195
views
2
answers
Comment: C: Trying to add ensembl_transcript_id using Biomart
... Hi benformatic, thanks for pointing this out. This basically voids everything that I'm trying to do and in light of this information, I should look for a way to run differential expression of 'transcripts' instead of genes. I'm not sure how to do that though. I was hoping that my output would conta ...
written 8 weeks ago by sandKings10
0
votes
2
answers
195
views
2
answers
Comment: C: Trying to add ensembl_transcript_id using Biomart
... Hi Mike, thanks so much. The '.' was the problem. ...
written 9 weeks ago by sandKings10
0
votes
2
answers
195
views
2
answers
Comment: C: Trying to add ensembl_transcript_id using Biomart
... Hi h.mon, thanks so much for the feedback. the line : y <- DGEList( counts = counts ) returns: Error in .isAllZero(counts) : counts must be positive finite values is the error because I have nonnumerical rows and columns values? I'll do some more research and try to troubleshoot this ...
written 9 weeks ago by sandKings10
2
votes
2
answers
195
views
5 follow
2
answers
Trying to add ensembl_transcript_id using Biomart
... Hi all, I'm trying to run a differential gene expression analysis where I want the report to contain ensemble_transcript_id as well. direc<- 'E:/counts_sep/MSC/' countFile<-paste(direc,'htseq.all.counts.txt',sep='') print("Loading count data") counts <- read.delim(file= ...
rnaseq biomart written 9 weeks ago by sandKings10 • updated 9 weeks ago by krushnach80420
0
votes
0
answers
382
views
0
answers
Comment: C: Help with Sanger Imputation Service
... Hi Kevin, sorry for the delay in getting back to you. My VCF header (?) looks like this before UCSC to ensemble conversion The complete list of contigs is too long and is exceeding the character limit for the post. However, apart from the standard contigs, ##contig= ##contig= ##co ...
written 10 weeks ago by sandKings10
0
votes
0
answers
382
views
0
answers
Comment: C: Help with Sanger Imputation Service
... Hi Kevin, I've sought help at GATk too but I'm afraid my incessant posts are wearing everyone down. Anyway, I'm following up with Michael's advise and trying to find the final build for GRCh37. I'm insisting on using GRCh37 because I find Sanger's interface more 'noob' friendly. ...
written 10 weeks ago by sandKings10
0
votes
1
answer
211
views
1
answers
Comment: C: Sanger Imputation Service - The input file sanity check failed : faidx_fetch_seq
... Hi Micheal, thank you so much for replying. I am using GRCh37 because Sanger Imputation Service requires that the coordinates are on GRCh37. I had everything mapped to GRCh38 but that took me down the path to using liftover files which I didn't want to do. Where can I find the final build for GRCh ...
written 10 weeks ago by sandKings10

Latest awards to sandKings

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: 2212 users visited in the last hour