User: robbenstijn

gravatar for robbenstijn
Reputation:
0
Status:
New User
Last seen:
1 month ago
Joined:
3 years, 9 months ago
Email:
r**********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by robbenstijn

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
95
views
1
answer
Trimmomatic installation makefile error
... I am trying to install this trimmomatic file on my remote server (linux): https://github.com/timflutre/trimmomatic Whenever I proceed with the install protocol and enter the `make` command (as specified in the README file) I get the following error: cd src/; javac -classpath ".:../lib/jbzip2-0 ...
trimmomatic makefile written 5 weeks ago by robbenstijn0 • updated 5 weeks ago by Pierre Lindenbaum131k
0
votes
1
answer
131
views
1
answers
Comment: C: Size difference BigWig vs. BedGraph files
... Thank you Pierre, I just ran the code and its output is 53195893894. I am not sure what this number means. Is it the number of characters, rows or mbs? ...
written 3 months ago by robbenstijn0
4
votes
1
answer
151
views
1
answer
Unkown NCBI genome chromosomes
... Hi everyone, I am trying to work with the GRCh38 (https://www-ncbi-nlm-nih-gov.tudelft.idm.oclc.org/genome/guide/human/#learn) from ncbi but i am encountering all sorts of chromosomes with which I am not familiar. Some examples to illustrate: chr11_KI270721v1_random chr19_KV575247v1_alt chr22_KQ7 ...
ncbi chromosome written 3 months ago by robbenstijn0 • updated 3 months ago by vkkodali2.2k
2
votes
1
answer
131
views
1
answer
Size difference BigWig vs. BedGraph files
... Hi everyone, I am trying to convert a 5.34 GB BigWig file to a BedGraph file using the bigWigToBedGraph tool for ucsc. Does anyone know how large the output file will be? Any help will be much appreciated. ...
bigwigtobedgraph bigwig written 4 months ago by robbenstijn0 • updated 4 months ago by Pierre Lindenbaum131k
0
votes
1
answer
290
views
1
answers
Comment: A: ucsc bigWigToBedGraph tool error
... You were right, I updated the system and everything works perfectly now. Thanks a lot ...
written 4 months ago by robbenstijn0
2
votes
1
answer
290
views
1
answer
ucsc bigWigToBedGraph tool error
... Hi Everyone, I am trying to convert a bigWig file to a BedGraph by using the bigWigToBedGraph tool. This failed when trying it in the local-Galaxy environment giving a fatal error 127: command not found (as can be seen in my previous post). I proceeded to get the tool directly from the ucsc directo ...
local galaxy bigwig ucsc written 4 months ago by robbenstijn0
2
votes
0
answers
182
views
0
answers
Galaxy - bigWigToBedGraph: command not found
... Hi everyone, I am trying to convert a BigWig file to a Bedgraph format by using local Galaxy. The tool that I added is called bigwig_to_bedgraph (https://toolshed.g2.bx.psu.edu/repository?repository_id=0dddb124b53a7bfd&changeset_revision=3799012ce2ff) and it was installed according to the Galax ...
bigwigtobedgraph galaxy bigwig written 4 months ago by robbenstijn0
0
votes
0
answers
156
views
0
answers
Comment: C: blastn not acknowledging "N" string.
... Thanks Pierre, I am not really sure what you mean. In the browserversion of BLAST, it should show results right? ...
written 4 months ago by robbenstijn0
1
vote
0
answers
156
views
0
answers
blastn not acknowledging "N" string.
... My sequence of CCNCCNTNNCCNC does not show any results when I use it as input in blastn on the human genome, although I am a 100% sure that results should come up. Changing the "N" string with any other of the nucleotide strings does give valid results, so I suspect that the tool just doesn't work u ...
nih blastn tool blast sequencing written 4 months ago by robbenstijn0
1
vote
1
answer
826
views
1
answer
Selecting relevant binding sites according to MACS data
... I've got ChIP-seq data analyzed with MACS and looks at such: > chr start end length summit tags -10log10(pvalue) fold_enrichment FDR(%) > chr1 9911 10616 706 251 77 60.46 4.07 0.30 > chr1 11119 11740 622 185 32 101.80 10.0 ...
macs peaks analysis written 3.8 years ago by robbenstijn0 • updated 3.7 years ago by le233670

Latest awards to robbenstijn

Great Question 3.7 years ago, created a question with more than 5,000 views. For BAM to BIGWIG
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Determine promoter regions relative to TSS.
Popular Question 3.7 years ago, created a question with more than 1,000 views. For BAM to BIGWIG

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour