User: James Ashmore

gravatar for James Ashmore
Reputation:
90
Status:
New User
Location:
London
Last seen:
5 years, 11 months ago
Joined:
6 years, 6 months ago
Email:
j******************@gmail.com

about me

Posts by James Ashmore

<prev • 23 results • page 1 of 3 • next >
0
votes
0
answers
5.0k
views
0
answers
Comment: C: How To Retrieve Chromosome Lengths Using Bsgenome Package?
... Hi Irsan, if I have interpreted your comment correctly, that creates a vector of the names but not in the order they appear in the NFKB object? Instead I have done the following and it appears to work : > library(BSgenome.Hsapiens.UCSC.hg19) > chr.lengths = seqlengths(Hsapiens)[1:25] > chr ...
written 6.1 years ago by James Ashmore90
0
votes
0
answers
5.0k
views
0
answers
Comment: C: How To Retrieve Chromosome Lengths Using Bsgenome Package?
... Hello, yes I just tried that now and it has worked, thankfully: > seqlengths(NFKB) chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 NA NA NA NA NA NA NA NA NA NA NA NA chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM ...
written 6.1 years ago by James Ashmore90
1
vote
0
answers
5.0k
views
5 follow
0
answers
How To Retrieve Chromosome Lengths Using Bsgenome Package?
... Hello, I am following along with the EBI's online course for ChIP-Seq analysis and have encountered an error when trying to retrieve chromosome lengths: > library(BSgenome.Hsapiens.UCSC.hg19) > seqlengths(NFKB) = seqlengths(Hsapiens) Error in .normargSeqlengths(value, seqnames(x)) : length ...
length chromosome written 6.1 years ago by James Ashmore90
0
votes
1
answer
2.8k
views
1
answers
Comment: C: Problem Compiling Velvet On Mac Osx
... Oh I see, thanks for the help! ...
written 6.1 years ago by James Ashmore90
0
votes
1
answer
2.8k
views
1
answers
Comment: C: Problem Compiling Velvet On Mac Osx
... I made the changes you suggested but much of the same warning messages still occur, with the final warning different from the one posted above: rm obj/*.o obj/dbg/*.o rm: obj/*.o: No such file or directory rm: obj/dbg/*.o: No such file or directory make: [cleanobj] Error 1 (ignored) mkdir -p obj g ...
written 6.1 years ago by James Ashmore90
2
votes
1
answer
2.8k
views
1
answer
Problem Compiling Velvet On Mac Osx
... Hello, I'm trying to compile Velvet on Mac OSX however I get the following error message: rm obj/*.o obj/dbg/*.o rm: obj/dbg/*.o: No such file or directory make: [cleanobj] Error 1 (ignored) mkdir -p obj gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString ...
velvet written 6.1 years ago by James Ashmore90 • updated 6.1 years ago by John Marshall1.8k
0
votes
0
answers
2.2k
views
0
answers
Comment: C: How Can I Stop Jackhammer Aligning The Same Target Sequence Multiple Times?
... Hi Sarah, Thank you for the suggestions! I'm using the default settings which HMMER has configured for jackhmmer. The reason I would like it to only hit once is I aim to identify each cluster as a protein family. Having one sequence hit multiple times messes up the alignment of the family 'members ...
written 6.3 years ago by James Ashmore90
0
votes
0
answers
2.2k
views
0
answers
How Can I Stop Jackhammer Aligning The Same Target Sequence Multiple Times?
... Hello everyone, I am using jackhmmer to cluster a set of protein sequences into groups. I am taking my 273 sequences, removing one and using that as the query against the 272 remaining sequences. Any hits which are found from the first query are removed from the pool for subsequent queries. The ali ...
alignment written 6.3 years ago by James Ashmore90 • updated 6.1 years ago by Biostar ♦♦ 20
1
vote
1
answer
1.4k
views
1
answer
Literature Mining For Domains Involved In Regeneration
... Hello everyone, I have a list of around 500 Pfam-A domains and I would like to mine the current literature for any involvement of proteins containing these domains in regeneration. The best option I have come up with so far is to enter the protein sequence into STITCH and get results from there, ho ...
domain literature written 6.4 years ago by James Ashmore90 • updated 3.4 years ago by Biostar ♦♦ 20
0
votes
2
answers
7.3k
views
2
answers
Comment: C: How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Archi
... Yes exactly, it means a combination of domains (in any order or in a specific order) not identified previously. For example on the Pfam database they list the types of architectures where the DDE domain has been found (http://pfam.sanger.ac.uk//family/PF13359.1#tabview=tab1). If you scroll down the ...
written 6.4 years ago by James Ashmore90

Latest awards to James Ashmore

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: 2275 users visited in the last hour