User: robbenstijn
robbenstijn • 0
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Posts by robbenstijn
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... 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 ...
written 5 weeks ago by
robbenstijn • 0
• updated
5 weeks ago by
Pierre Lindenbaum ♦ 131k
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... 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
robbenstijn • 0
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... 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 ...
written 3 months ago by
robbenstijn • 0
• updated
3 months ago by
vkkodali • 2.2k
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... 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. ...
written 4 months ago by
robbenstijn • 0
• updated
4 months ago by
Pierre Lindenbaum ♦ 131k
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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
robbenstijn • 0
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... 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 ...
written 4 months ago by
robbenstijn • 0
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... 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 ...
written 4 months ago by
robbenstijn • 0
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... 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
robbenstijn • 0
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... 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 ...
written 4 months ago by
robbenstijn • 0
1
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... 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 ...
written 3.8 years ago by
robbenstijn • 0
• updated
3.7 years ago by
le2336 • 70
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For Determine promoter regions relative to TSS.
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