User: b.verhagen

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b.verhagen0
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Posts by b.verhagen

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Comment: C: Peptide Blast on MS/MS Spectra Databases
... I don't think so.. as I would like to validate whether the spectrum, corresponding to the peptide sequence, is already present in the depository/database, prior to the real mass spec experiment. ...
written 14 days ago by b.verhagen0
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Peptide Blast on MS/MS Spectra Databases
... Hi, I was wondering whether the peptide sequences that correspond to mass spectra, deposited in spectra databases, can be obtained somewhere? Best regards, Bram Verhagen ...
proteomics reference spectra library ms/ms written 14 days ago by b.verhagen0
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Comment: A: STAR Create Custom Refence Genome
... Now I wrote the following script (script.sh): #!/bin/bash /home/hub_tanenbaum/bverhagen /STAR/source/STAR --runMode genomeGenerate –genomeDir /hpc/hub_tanenbaum/Bram/ --genomeFastaFiles /hpc/hub_tanenbaum/Bram/sequence.fa And submitted it with the following command: qsub -q all.q -l ...
written 10 weeks ago by b.verhagen0 • updated 10 weeks ago by genomax62k
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Comment: C: STAR Create Custom Refence Genome
... I am running the script on a HPC server using a mobile terminal (5GB RAM on server). The library is not very big though, roughly 8000 sequences. ...
written 10 weeks ago by b.verhagen0
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Comment: C: STAR Create Custom Refence Genome
... Thanks, However after changing this, I obtain the following: Dec 04 14:43:26 ... starting to generate Genome files terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted ...
written 10 weeks ago by b.verhagen0
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STAR Create Custom Refence Genome
... Dear all, I want to use STAR to align my reads to a small reference genome (~12.500 UTRs). Although I have created a .fa-file of my library STAR is not able to generate a genome, as it is unable to read the file. I was wondering if anyone else has experienced the same problem? Or whether anyone ha ...
star rna-seq written 10 weeks ago by b.verhagen0
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RCAS Motif Discovery
... Hi all, I am trying to discover whether certain RNA molecules contain a motif. I am currently using the RCAS Package in R. Although, I do not have a problem with identifying motifs in the coding sequence, I, so far, have not been able to unravel any sequence motifs in the UTRs. When running runM ...
motif discovery rna written 7 months ago by b.verhagen0 • updated 5 months ago by Biostar ♦♦ 20

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